From b518dfe7f49f66dec387b31aacb739e67b55a2c6 Mon Sep 17 00:00:00 2001 From: Colin Date: Sun, 16 Jun 2024 22:43:02 -0400 Subject: [PATCH] Only snap error --- .../__snapshots__/add-assembly.test.ts.snap | 123 +- .../__snapshots__/add-connection.test.ts.snap | 221 +- .../__snapshots__/add-track.test.ts.snap | 1586 +- .../__snapshots__/admin-server.test.ts.snap | 24 +- .../__snapshots__/create.test.ts.snap | 42605 +--------------- .../set-default-session.test.ts.snap | 48 +- .../__snapshots__/text-index.test.ts.snap | 21355 +------- .../__snapshots__/upgrade.test.ts.snap | 48 +- .../src/commands/add-assembly.test.ts | 20 +- .../src/commands/add-connection.test.ts | 61 +- .../src/commands/add-track.test.ts | 58 +- .../src/commands/admin-server-test-utils.ts | 29 - .../src/commands/admin-server.test.ts | 35 +- .../jbrowse-cli/src/commands/create.test.ts | 12 +- .../src/commands/set-default-session.test.ts | 8 +- .../src/commands/text-index.test.ts | 4 +- .../jbrowse-cli/src/commands/upgrade.test.ts | 8 +- 17 files changed, 678 insertions(+), 65567 deletions(-) delete mode 100644 products/jbrowse-cli/src/commands/admin-server-test-utils.ts diff --git a/products/jbrowse-cli/src/commands/__snapshots__/add-assembly.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/add-assembly.test.ts.snap index 5d4b35ba32..5912a0fcba 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/add-assembly.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/add-assembly.test.ts.snap @@ -1,16 +1,6 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`add-assembly no load flag 1`] = ` -{ - "code": undefined, - "message": "Please specify the loading operation for this file with --load copy|symlink|move|inPlace", - "oclif": { - "exit": 110, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`add-assembly no load flag 1`] = `"Please specify the loading operation for this file with --load copy|symlink|move|inPlace"`; exports[`adds an assembly from a 2bit 1`] = ` { @@ -522,116 +512,23 @@ exports[`can use an existing config file 1`] = ` } `; -exports[`fails if custom refNameAliases adapter has no type 1`] = ` -{ - "code": undefined, - "message": "No "type" specified in refNameAliases adapter "{}"", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if custom refNameAliases adapter has no type 1`] = `"No "type" specified in refNameAliases adapter "{}""`; -exports[`fails if custom refNameAliases adapter has no type 2`] = ` -{ - "code": undefined, - "message": "No "type" specified in refNameAliases adapter "{}"", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if custom refNameAliases adapter has no type 2`] = `"No "type" specified in refNameAliases adapter "{}""`; -exports[`fails if custom sequence adapter has no type 1`] = ` -{ - "code": undefined, - "message": "No "type" specified in sequence adapter "{}"", - "oclif": { - "exit": 140, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if custom sequence adapter has no type 1`] = `"No "type" specified in sequence adapter "{}""`; -exports[`fails if it cannot find a file 1`] = ` -{ - "code": undefined, - "message": "Could not resolve to a file or a URL: "simple.doesNotExist.fasta"", - "oclif": { - "exit": 40, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if it cannot find a file 1`] = `"Could not resolve to a file or a URL: "simple.doesNotExist.fasta""`; -exports[`fails if it cannot guess the sequence type 1`] = ` -{ - "code": undefined, - "message": "Could not determine sequence type automatically, add --type to specify it", - "oclif": { - "exit": 170, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if it cannot guess the sequence type 1`] = `"Could not determine sequence type automatically, add --type to specify it"`; -exports[`fails if load flag is passed with a URL 1`] = ` -{ - "code": undefined, - "message": "URL detected with --load flag. Please rerun the function without the --load flag", - "oclif": { - "exit": 120, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if load flag is passed with a URL 1`] = `"URL detected with --load flag. Please rerun the function without the --load flag"`; -exports[`fails if trying to add an assembly with a name that already exists 1`] = ` -{ - "code": undefined, - "message": "Cannot add assembly with name simple, an assembly with that name already exists", - "oclif": { - "exit": 160, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if trying to add an assembly with a name that already exists 1`] = `"Cannot add assembly with name simple, an assembly with that name already exists"`; -exports[`fails if using inline JSON sequence custom with no --name 1`] = ` -{ - "code": undefined, - "message": "Must provide --name when using custom inline JSON sequence", - "oclif": { - "exit": 130, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if using inline JSON sequence custom with no --name 1`] = `"Must provide --name when using custom inline JSON sequence"`; -exports[`fails if using invalid inline JSON 1`] = ` -{ - "code": undefined, - "message": "Error: ENOENT: no such file or directory, open 'notValidJSON'", - "oclif": { - "exit": 40, - }, - "skipOclifErrorHandling": undefined, - "suggestions": [ - "Make sure the file "notValidJSON" exists or use --out to point to a directory with a config.json", - "Run \`jbrowse add-assembly\` to create a config file", - ], -} -`; +exports[`fails if using invalid inline JSON 1`] = `"Error: ENOENT: no such file or directory, open 'notValidJSON'"`; exports[`relative path 1`] = ` { diff --git a/products/jbrowse-cli/src/commands/__snapshots__/add-connection.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/add-connection.test.ts.snap index 0b11ba09c1..23158fbde4 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/add-connection.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/add-connection.test.ts.snap @@ -1,204 +1,71 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adds JBrowse1 connection from a url 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [ - { - "connectionId": "JBrowse1Connection-1", - "dataDirLocation": { - "locationType": "UriLocation", - "uri": "https://mysite.com/jbrowse/data", - }, - "name": "JBrowse1Connection-1", - "type": "JBrowse1Connection", +[ + { + "connectionId": "JBrowse1Connection-1", + "dataDirLocation": { + "locationType": "UriLocation", + "uri": "https://mysite.com/jbrowse/data", }, - ], - "defaultSession": { - "name": "New Session", + "name": "JBrowse1Connection-1", + "type": "JBrowse1Connection", }, - "tracks": [], -} +] `; exports[`adds a custom connection with user set fields 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [ - { - "assemblyNames": [ - "testAssembly", - ], - "connectionId": "newConnectionId", - "locationType": "UriLocation", - "name": "newName", - "type": "newType", - "url": { - "uri": "https://mysite.com/custom", - }, +[ + { + "assemblyNames": [ + "testAssembly", + ], + "connectionId": "newConnectionId", + "locationType": "UriLocation", + "name": "newName", + "type": "newType", + "url": { + "uri": "https://mysite.com/custom", }, - ], - "defaultSession": { - "name": "New Session", }, - "tracks": [], -} +] `; exports[`adds an UCSCTrackHubConnection connection from a url 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [ - { - "connectionId": "UCSCTrackHubConnection-1", - "hubTxtLocation": { - "locationType": "UriLocation", - "uri": "https://mysite.com/data/hub.txt", - }, - "name": "UCSCTrackHubConnection-1", - "type": "UCSCTrackHubConnection", +[ + { + "connectionId": "UCSCTrackHubConnection-1", + "hubTxtLocation": { + "locationType": "UriLocation", + "uri": "https://mysite.com/data/hub.txt", }, - ], - "defaultSession": { - "name": "New Session", + "name": "UCSCTrackHubConnection-1", + "type": "UCSCTrackHubConnection", }, - "tracks": [], -} +] `; -exports[`fails if data directory is not an url 1`] = ` -{ - "code": undefined, - "message": "The location provided is not a valid URL", - "oclif": { - "exit": 160, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if data directory is not an url 1`] = `"The location provided is not a valid URL"`; -exports[`fails if no config file 1`] = ` -{ - "code": undefined, - "message": "Error: ENOENT: no such file or directory, open './config.json'", - "oclif": { - "exit": 40, - }, - "skipOclifErrorHandling": undefined, - "suggestions": [ - "Make sure the file "./config.json" exists or use --out to point to a directory with a config.json", - "Run \`jbrowse add-assembly\` to create a config file", - ], -} -`; +exports[`fails if no config file 1`] = `"Error: ENOENT: no such file or directory, open './config.json'"`; exports[`fails to add a duplicate connection 1`] = ` -{ - "code": undefined, - "message": "Cannot add connection with id newConnectionId, a connection with that id already exists. -Use --overwrite if you would like to replace the existing connection", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"Cannot add connection with id newConnectionId, a connection with that id already exists. +Use --overwrite if you would like to replace the existing connection" `; -exports[`fails when fetching from url fails 1`] = ` -{ - "code": undefined, - "message": "Unable to fetch from URL, Error: Response returned with code 500", - "oclif": { - "exit": 170, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails when fetching from url fails 1`] = `"Unable to fetch from URL, Error: Response returned with code 500"`; exports[`overwrites an existing custom connection and does not check URL 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [ - { - "connectionId": "newConnectionId", - "locationType": "UriLocation", - "name": "newConnectionId", - "type": "custom", - "url": { - "uri": "https://mysite.com/custom", - }, +[ + { + "connectionId": "newConnectionId", + "locationType": "UriLocation", + "name": "newConnectionId", + "type": "custom", + "url": { + "uri": "https://mysite.com/custom", }, - ], - "defaultSession": { - "name": "New Session", }, - "tracks": [], -} +] `; diff --git a/products/jbrowse-cli/src/commands/__snapshots__/add-track.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/add-track.test.ts.snap index 791372f169..07be5e7e57 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/add-track.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/add-track.test.ts.snap @@ -1,1246 +1,666 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`adds a bam track from a url 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "https://mysite.com/data/simple.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "https://mysite.com/data/simple.bam.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "https://mysite.com/data/simple.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "https://mysite.com/data/simple.bam.bai", - }, + "uri": "test.2bit", }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with all the custom fields 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "simple.bam", + }, + "index": { + "indexType": "BAI", + "location": { "locationType": "UriLocation", - "uri": "simple.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "simple.bam.bai", - }, - }, - "type": "BamAdapter", - }, - "assemblyNames": [ - "customAssemblyName", - ], - "category": [ - "newcategory", - ], - "defaultRendering": "test", - "description": "new description", - "name": "customName", - "trackId": "customTrackId", - "type": "CustomTrackType", - }, - ], -} + "uri": "simple.bam.bai", + }, + }, + "type": "BamAdapter", + }, + "assemblyNames": [ + "customAssemblyName", + ], + "category": [ + "newcategory", + ], + "defaultRendering": "test", + "description": "new description", + "name": "customName", + "trackId": "customTrackId", + "type": "CustomTrackType", + }, +] `; exports[`adds a bam track with bai 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "simple.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "simple.bam.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "simple.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "simple.bam.bai", - }, - }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", + "uri": "test.2bit", }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with csi 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "simple.bam", + }, + "index": { + "indexType": "CSI", + "location": { + "locationType": "UriLocation", + "uri": "simple.bam.csi", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "simple.bam", - }, - "index": { - "indexType": "CSI", - "location": { - "locationType": "UriLocation", - "uri": "simple.bam.csi", - }, + "uri": "test.2bit", }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with indexFile for bai 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "simple.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "simple.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "simple.bam", + "uri": "test.2bit", }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "simple.bai", - }, - }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with load inPlace 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "/testing/in/place.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "/testing/in/place.bam.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "/testing/in/place.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "/testing/in/place.bam.bai", - }, - }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", + "uri": "test.2bit", }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "place", - "trackId": "place", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "place", + "trackId": "place", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with subDir 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "bam/simple.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "bam/simple.bam.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "bam/simple.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "bam/simple.bam.bai", - }, + "uri": "test.2bit", }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam track with subDir and localPath protocol 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { - "localPath": "bam/simple.bam", +[ + { + "adapter": { + "bamLocation": { + "localPath": "bam/simple.bam", + "locationType": "LocalPathLocation", + }, + "index": { + "indexType": "BAI", + "location": { + "localPath": "bam/simple.bam.bai", "locationType": "LocalPathLocation", }, - "index": { - "indexType": "BAI", - "location": { - "localPath": "bam/simple.bam.bai", - "locationType": "LocalPathLocation", - }, - }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", + }, + "sequenceAdapter": { + "twoBitLocation": { + "locationType": "UriLocation", + "uri": "test.2bit", }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "simple", - "trackId": "simple", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "simple", + "trackId": "simple", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a bam+bai track with load inPlace 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", +[ + { + "adapter": { + "bamLocation": { + "locationType": "UriLocation", + "uri": "/testing/in/place.bam", + }, + "index": { + "indexType": "BAI", + "location": { + "locationType": "UriLocation", + "uri": "/something/else/random.bai", }, - "trackId": "", - "type": "testSequenceTrack", }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "bamLocation": { + "sequenceAdapter": { + "twoBitLocation": { "locationType": "UriLocation", - "uri": "/testing/in/place.bam", - }, - "index": { - "indexType": "BAI", - "location": { - "locationType": "UriLocation", - "uri": "/something/else/random.bai", - }, + "uri": "test.2bit", }, - "sequenceAdapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "type": "BamAdapter", + "type": "testSeqAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "place", - "trackId": "place", - "type": "AlignmentsTrack", + "type": "BamAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "place", + "trackId": "place", + "type": "AlignmentsTrack", + }, +] `; exports[`adds a chain file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "chainLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.chain", - }, - "type": "ChainAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels", - "trackId": "volvox_inv_indels", - "type": "SyntenyTrack", - }, - ], -} + "chainLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.chain", + }, + "type": "ChainAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, +] `; exports[`adds a delta file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "deltaLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.delta", - }, - "type": "DeltaAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels", - "trackId": "volvox_inv_indels", - "type": "SyntenyTrack", - }, - ], -} + "deltaLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.delta", + }, + "type": "DeltaAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, +] `; exports[`adds a mashmap file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "outLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.out", - }, - "type": "MashMapAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels", - "trackId": "volvox_inv_indels", - "type": "SyntenyTrack", - }, - ], -} + "outLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.out", + }, + "type": "MashMapAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, +] `; exports[`adds a mcscan anchors file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "bed1Location": { - "locationType": "UriLocation", - "uri": "grape.bed", - }, - "bed2Location": { - "locationType": "UriLocation", - "uri": "peach.bed", - }, - "mcscanAnchorsLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.anchors", - }, - "type": "MCScanAnchorsAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels", - "trackId": "volvox_inv_indels", - "type": "SyntenyTrack", - }, - ], -} + "bed1Location": { + "locationType": "UriLocation", + "uri": "grape.bed", + }, + "bed2Location": { + "locationType": "UriLocation", + "uri": "peach.bed", + }, + "mcscanAnchorsLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.anchors", + }, + "type": "MCScanAnchorsAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, +] `; exports[`adds a mcscan simple anchors file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "bed1Location": { - "locationType": "UriLocation", - "uri": "grape.bed", - }, - "bed2Location": { - "locationType": "UriLocation", - "uri": "peach.bed", - }, - "mcscanSimpleAnchorsLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.anchors.simple", - }, - "type": "MCScanSimpleAnchorsAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels.anchors", - "trackId": "volvox_inv_indels.anchors", - "type": "SyntenyTrack", - }, - ], -} + "bed1Location": { + "locationType": "UriLocation", + "uri": "grape.bed", + }, + "bed2Location": { + "locationType": "UriLocation", + "uri": "peach.bed", + }, + "mcscanSimpleAnchorsLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.anchors.simple", + }, + "type": "MCScanSimpleAnchorsAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels.anchors", + "trackId": "volvox_inv_indels.anchors", + "type": "SyntenyTrack", + }, +] `; exports[`adds a paf file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "pafLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.paf", - }, - "type": "PAFAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels", - "trackId": "volvox_inv_indels", - "type": "SyntenyTrack", - }, - ], -} + "pafLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.paf", + }, + "type": "PAFAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels", + "trackId": "volvox_inv_indels", + "type": "SyntenyTrack", + }, +] `; exports[`adds a paf.gz file 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "assemblyNames": [ - "volvox_random_inv", - "volvox", - ], - "pafLocation": { - "locationType": "UriLocation", - "uri": "volvox_inv_indels.paf.gz", - }, - "type": "PAFAdapter", - }, +[ + { + "adapter": { "assemblyNames": [ "volvox_random_inv", "volvox", ], - "name": "volvox_inv_indels.paf", - "trackId": "volvox_inv_indels.paf", - "type": "SyntenyTrack", - }, - ], -} + "pafLocation": { + "locationType": "UriLocation", + "uri": "volvox_inv_indels.paf.gz", + }, + "type": "PAFAdapter", + }, + "assemblyNames": [ + "volvox_random_inv", + "volvox", + ], + "name": "volvox_inv_indels.paf", + "trackId": "volvox_inv_indels.paf", + "type": "SyntenyTrack", + }, +] `; exports[`adds a plaintext bed 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", +[ + { + "adapter": { + "bedLocation": { + "locationType": "UriLocation", + "uri": "volvox.bed", + }, + "type": "BedAdapter", + }, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox", + "trackId": "volvox", + "type": "FeatureTrack", }, - "tracks": [ - { - "adapter": { - "bedLocation": { - "locationType": "UriLocation", - "uri": "volvox.bed", - }, - "type": "BedAdapter", - }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox", - "trackId": "volvox", - "type": "FeatureTrack", - }, - ], -} +] `; exports[`adds a plaintext bedpe 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", +[ + { + "adapter": { + "bedpeLocation": { + "locationType": "UriLocation", + "uri": "volvox.bedpe", + }, + "type": "BedpeAdapter", + }, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox", + "trackId": "volvox", + "type": "VariantTrack", }, - "tracks": [ - { - "adapter": { - "bedpeLocation": { - "locationType": "UriLocation", - "uri": "volvox.bedpe", - }, - "type": "BedpeAdapter", - }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox", - "trackId": "volvox", - "type": "VariantTrack", - }, - ], -} +] `; exports[`adds a plaintext gff 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", +[ + { + "adapter": { + "gffLocation": { + "locationType": "UriLocation", + "uri": "volvox.sort.gff3", + }, + "type": "Gff3Adapter", + }, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox.sort", + "trackId": "volvox.sort", + "type": "FeatureTrack", }, - "tracks": [ - { - "adapter": { - "gffLocation": { - "locationType": "UriLocation", - "uri": "volvox.sort.gff3", - }, - "type": "Gff3Adapter", - }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox.sort", - "trackId": "volvox.sort", - "type": "FeatureTrack", - }, - ], -} +] `; exports[`adds a plaintext gtf 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", +[ + { + "adapter": { + "gtfLocation": { + "locationType": "UriLocation", + "uri": "volvox.sorted.gtf", + }, + "type": "GtfAdapter", + }, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox.sorted", + "trackId": "volvox.sorted", + "type": "FeatureTrack", }, - "tracks": [ - { - "adapter": { - "gtfLocation": { - "locationType": "UriLocation", - "uri": "volvox.sorted.gtf", - }, - "type": "GtfAdapter", - }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox.sorted", - "trackId": "volvox.sorted", - "type": "FeatureTrack", - }, - ], -} +] `; exports[`adds a plaintext vcf 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", +[ + { + "adapter": { + "type": "VcfAdapter", + "vcfLocation": { + "locationType": "UriLocation", + "uri": "volvox.filtered.vcf", + }, + }, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox.filtered", + "trackId": "volvox.filtered", + "type": "VariantTrack", }, - "tracks": [ - { - "adapter": { - "type": "VcfAdapter", - "vcfLocation": { - "locationType": "UriLocation", - "uri": "volvox.filtered.vcf", - }, - }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox.filtered", - "trackId": "volvox.filtered", - "type": "VariantTrack", - }, - ], -} +] `; exports[`adds a tabix gff with csi 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "gffGzLocation": { +[ + { + "adapter": { + "gffGzLocation": { + "locationType": "UriLocation", + "uri": "volvox.sort.gff3.gz", + }, + "index": { + "indexType": "CSI", + "location": { "locationType": "UriLocation", - "uri": "volvox.sort.gff3.gz", + "uri": "volvox.sort.gff3.gz.csi", }, - "index": { - "indexType": "CSI", - "location": { - "locationType": "UriLocation", - "uri": "volvox.sort.gff3.gz.csi", - }, - }, - "type": "Gff3TabixAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox.sort.gff3", - "trackId": "volvox.sort.gff3", - "type": "FeatureTrack", + "type": "Gff3TabixAdapter", }, - ], -} + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox.sort.gff3", + "trackId": "volvox.sort.gff3", + "type": "FeatureTrack", + }, +] `; exports[`adds a tabix gff with tbi 1`] = ` -{ - "assemblies": [ - { - "name": "testAssembly", - "sequence": { - "adapter": { - "twoBitLocation": { - "locationType": "UriLocation", - "uri": "test.2bit", - }, - "type": "testSeqAdapter", - }, - "trackId": "", - "type": "testSequenceTrack", - }, - }, - ], - "configuration": {}, - "connections": [], - "defaultSession": { - "name": "New Session", - }, - "tracks": [ - { - "adapter": { - "gffGzLocation": { +[ + { + "adapter": { + "gffGzLocation": { + "locationType": "UriLocation", + "uri": "volvox.sort.gff3.gz", + }, + "index": { + "indexType": "TBI", + "location": { "locationType": "UriLocation", - "uri": "volvox.sort.gff3.gz", - }, - "index": { - "indexType": "TBI", - "location": { - "locationType": "UriLocation", - "uri": "volvox.sort.gff3.gz.tbi", - }, + "uri": "volvox.sort.gff3.gz.tbi", }, - "type": "Gff3TabixAdapter", }, - "assemblyNames": [ - "testAssembly", - ], - "name": "volvox.sort.gff3", - "trackId": "volvox.sort.gff3", - "type": "FeatureTrack", + "type": "Gff3TabixAdapter", }, - ], -} -`; - -exports[`cannot add a track if there is no config file 1`] = ` -{ - "code": undefined, - "message": "Error: ENOENT: no such file or directory, open './config.json'", - "oclif": { - "exit": 40, + "assemblyNames": [ + "testAssembly", + ], + "name": "volvox.sort.gff3", + "trackId": "volvox.sort.gff3", + "type": "FeatureTrack", }, - "skipOclifErrorHandling": undefined, - "suggestions": [ - "Make sure the file "./config.json" exists or use --out to point to a directory with a config.json", - "Run \`jbrowse add-assembly\` to create a config file", - ], -} +] `; -exports[`cannot add a track with the same track id 1`] = ` -{ - "code": undefined, - "message": "Cannot add track with id simple, a track with that id already exists (use --force to override)", - "oclif": { - "exit": 160, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`cannot add a track if there is no config file 1`] = `"Error: ENOENT: no such file or directory, open './config.json'"`; -exports[`fails if URL with load flag is passed 1`] = ` -{ - "code": undefined, - "message": "The --load flag is used for local files only, but a URL was provided", - "oclif": { - "exit": 100, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`cannot add a track with the same track id 1`] = `"Cannot add track with id simple, a track with that id already exists (use --force to override)"`; -exports[`fails if it cannot assume the assemblyname 1`] = ` -{ - "code": undefined, - "message": "No assemblies found. Please add one before adding tracks", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if URL with load flag is passed 1`] = `"The --load flag is used for local files only, but a URL was provided"`; + +exports[`fails if it cannot assume the assemblyname 1`] = `"No assemblies found. Please add one before adding tracks"`; exports[`fails if load flag is not passed in for a localFile 1`] = ` -{ - "code": undefined, - "message": "The --load flag should be used if a local file is used, example --load +"The --load flag should be used if a local file is used, example --load copy to copy the file into the config directory. Options for load are - copy/move/symlink/inPlace (inPlace for no file operations)", - "oclif": { - "exit": 110, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} + copy/move/symlink/inPlace (inPlace for no file operations)" `; exports[`fails if no track is specified 1`] = ` @@ -1249,14 +669,4 @@ track Track file or URL See more help with --help" `; -exports[`fails multiple assemblies exist but no assemblyNames passed 1`] = ` -{ - "code": undefined, - "message": "Too many assemblies, cannot default to one. Please specify the assembly with the --assemblyNames flag", - "oclif": { - "exit": 2, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails multiple assemblies exist but no assemblyNames passed 1`] = `"Too many assemblies, cannot default to one. Please specify the assembly with the --assemblyNames flag"`; diff --git a/products/jbrowse-cli/src/commands/__snapshots__/admin-server.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/admin-server.test.ts.snap index b5d33b0473..6e21135b71 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/admin-server.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/admin-server.test.ts.snap @@ -39,26 +39,6 @@ exports[`does not overwrite an existing config 1`] = ` } `; -exports[`throws an error with a negative port 1`] = ` -{ - "code": undefined, - "message": "-10 is not a valid port", - "oclif": { - "exit": 2, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`throws an error with a negative port 1`] = `"-10 is not a valid port"`; -exports[`throws an error with a port greater than 65535 1`] = ` -{ - "code": undefined, - "message": "66666 is not a valid port", - "oclif": { - "exit": 2, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`throws an error with a port greater than 65535 1`] = `"66666 is not a valid port"`; diff --git a/products/jbrowse-cli/src/commands/__snapshots__/create.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/create.test.ts.snap index 041116b997..03e003233d 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/create.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/create.test.ts.snap @@ -1,42612 +1,21 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`fails because this directory is already set up 1`] = ` -{ - "code": undefined, - "message": "jbrowse This directory has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files", - "oclif": { - "exit": 120, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails because this directory is already set up 1`] = `"jbrowse This directory has existing files and could cause conflicts with create. Please choose another directory or use the force flag to overwrite existing files"`; exports[`fails if no path is provided to the command 1`] = ` -{ - "args": [ - { - "description": "Location where JBrowse 2 will be installed", - "input": [], - "name": "localPath", - "parse": [Function], - "required": true, - "type": "option", - }, - ], - "code": undefined, - "message": "Missing 1 required arg: +"Missing 1 required arg: localPath Location where JBrowse 2 will be installed -See more help with --help", - "oclif": { - "exit": 2, - }, - "parse": { - "input": { - "--": undefined, - "args": { - "localPath": { - "description": "Location where JBrowse 2 will be installed", - "input": [], - "name": "localPath", - "parse": [Function], - "required": true, - "type": "option", - }, - }, - "argv": [], - "context": Create { - "argv": [], - "config": Config { - "_base": "@oclif/core@4.0.6", - "_commandIDs": undefined, - "_commands": Map { - "add-assembly" => { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection" => { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - 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"args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. 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"summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - 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"delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "upgrade" => { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "help" => { - "aliasPermutations": [], - "aliases": [], - "args": { - "command": { - "description": "Command to show help for.", - "name": "command", - "required": false, - }, - }, - "description": "Display help for <%= config.bin %>.", - "enableJsonFlag": false, - "flags": { - "nested-commands": { - "allowNo": false, - "char": "n", - "description": "Include all nested commands in the output.", - "name": "nested-commands", - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hiddenAliases": [], - "id": "help", - "isESM": true, - "load": [Function], - "permutations": [ - "help", - ], - "pluginAlias": "@oclif/plugin-help", - "pluginName": "@oclif/plugin-help", - "pluginType": "core", - "relativePath": [ - "lib", - "commands", - "help.js", - ], - "strict": false, - }, - }, - "_topics": Map { - "add-assembly" => { - "description": "Add an assembly to a JBrowse 2 configuration", - "name": "add-assembly", - }, - "add-connection" => { - "description": "Add a connection to a JBrowse 2 configuration", - "name": "add-connection", - }, - "add-track" => { - "description": "Add a track to a JBrowse 2 configuration", - "name": "add-track", - }, - "add-track-json" => { - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "name": "add-track-json", - }, - "admin-server" => { - "description": "Start up a small admin server for JBrowse configuration", - "name": "admin-server", - }, - "create" => { - "description": "Downloads and installs the latest JBrowse 2 release", - "name": "create", - }, - "make-pif" => { - "description": "creates pairwise indexed PAF (PIF), with bgzip and tabix", - "name": "make-pif", - }, - "remove-track" => { - "description": "Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!", - "name": "remove-track", - }, - "set-default-session" => { - "description": "Set a default session with views and tracks", - "name": "set-default-session", - }, - "sort-gff" => { - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "name": "sort-gff", - }, - "text-index" => { - "description": "Make a text-indexing file for any given track(s).", - "name": "text-index", - }, - "upgrade" => { - "description": "Upgrades JBrowse 2 to latest version", - "name": "upgrade", - }, - "help" => { - "description": "Display help for <%= config.bin %>.", - "name": "help", - }, - }, - "arch": "x64", - "bin": "jbrowse", - "binAliases": undefined, - "binPath": undefined, - "cacheDir": "/home/cdiesh/.cache/@jbrowse/cli", - "channel": "stable", - "commandPermutations": Map { - "add-assembly" => Set { - "add-assembly", - }, - "add-connection" => Set { - "add-connection", - }, - "add-track" => Set { - "add-track", - }, - "add-track-json" => Set { - "add-track-json", - }, - "admin-server" => Set { - "admin-server", - }, - "create" => Set { - "create", - }, - "make-pif" => Set { - "make-pif", - }, - "remove-track" => Set { - "remove-track", - }, - "set-default-session" => Set { - "set-default-session", - }, - "sort-gff" => Set { - "sort-gff", - }, - "text-index" => Set { - "text-index", - }, - "upgrade" => Set { - "upgrade", - }, - "help" => Set { - "help", - }, - }, - "configDir": "/home/cdiesh/.config/@jbrowse/cli", - "dataDir": "/home/cdiesh/.local/share/@jbrowse/cli", - "dirname": "@jbrowse/cli", - "flexibleTaxonomy": false, - "home": "/home/cdiesh", - "isSingleCommandCLI": false, - "name": "@jbrowse/cli", - "npmRegistry": undefined, - "nsisCustomization": undefined, - "options": { - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - "decompress": "^4.0.0", - "express": "^4.17.1", - "ixixx": "^2.0.1", - "json-parse-better-errors": "^1.0.2", - "node-fetch-native": "^1.6.4", - "rimraf": "^5.0.0", - "tslib": "^2.3.1", - }, - "description": "A command line tool for working with JBrowse 2", - "devDependencies": { - "typescript": "^5.1.3", - }, - "engines": { - "node": ">=16", - }, - "files": [ - "/bin", - "/lib", - "/npm-shrinkwrap.json", - "/oclif.manifest.json", - ], - "homepage": "https://jbrowse.org", - "keywords": [ - "jbrowse", - "jbrowse2", - "oclif", - ], - "license": "Apache-2.0", - "main": "lib/index.js", - "name": "@jbrowse/cli", - "oclif": { - "bin": "jbrowse", - "commands": "./lib/commands", - "plugins": [ - "@oclif/plugin-help", - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>", - }, - "publishConfig": { - "access": "public", - }, - "repository": { - "directory": "products/jbrowse-cli", - "type": "git", - "url": "https://github.com/GMOD/jbrowse-components.git", - }, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "platform": "linux", - "pluginLoader": PluginLoader { - "errors": [], - "options": { - "plugins": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "plugins": Map { - "@jbrowse/cli" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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"hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - 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Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - 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"helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - 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"env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - "", - "# List available versions", - "$ jbrowse create --listVersions", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing JBrowse 2 installation if present in path", - 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"deprecated": undefined, - "description": "Version of JBrowse 2 to install. 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"description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - 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"delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. 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"relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "create": { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "set-default-session": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - "examples": [ - "$ jbrowse set-default-session --session /path/to/default/session.json", - "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json", - "$ jbrowse set-default-session --view LinearGenomeView, --name newName", - "$ jbrowse set-default-session --currentSession # Prints out current default session", - ], - "flags": { - "currentSession": { - "aliases": undefined, - "allowNo": false, - "char": "c", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "List out the current default session", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "currentSession", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "delete": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Delete any existing default session.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "delete", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": "New Default Session", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff": { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. 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"summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - }, - "version": "2.11.2", - }, - "moduleType": "commonjs", - "name": "@jbrowse/cli", - "options": { - "isRoot": true, - "pjson": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "parent": undefined, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - 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}, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli", - "tag": undefined, - "type": "core", - "valid": true, - "version": "2.11.2", - }, - "@oclif/plugin-help" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@oclif/plugin-help", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - 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"rootPlugin": Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - 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Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. 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"hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - 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"env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - 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Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - }, - "version": "2.11.2", - }, - "moduleType": "commonjs", - "name": "@jbrowse/cli", - "options": { - "isRoot": true, - "pjson": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "parent": undefined, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - "decompress": "^4.0.0", - "express": "^4.17.1", - "ixixx": "^2.0.1", - "json-parse-better-errors": "^1.0.2", - "node-fetch-native": "^1.6.4", - "rimraf": "^5.0.0", - "tslib": "^2.3.1", - }, - "description": "A command line tool for working with JBrowse 2", - "devDependencies": { - "typescript": "^5.1.3", - }, - "engines": { - "node": ">=16", - }, - "files": [ - "/bin", - "/lib", - "/npm-shrinkwrap.json", - "/oclif.manifest.json", - ], - "homepage": "https://jbrowse.org", - "keywords": [ - "jbrowse", - "jbrowse2", - "oclif", - ], - "license": "Apache-2.0", - "main": "lib/index.js", - "name": "@jbrowse/cli", - "oclif": { - "bin": "jbrowse", - "commands": "./lib/commands", - "plugins": [ - "@oclif/plugin-help", - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>", - }, - "publishConfig": { - "access": "public", - }, - "repository": { - "directory": "products/jbrowse-cli", - "type": "git", - "url": "https://github.com/GMOD/jbrowse-components.git", - }, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli", - "tag": undefined, - "type": "core", - "valid": true, - "version": "2.11.2", - }, - "shell": "zsh", - "theme": undefined, - "topicPermutations": Map {}, - "topicSeparator": ":", - "updateConfig": { - "node": {}, - "s3": { - "bucket": undefined, - "host": undefined, - "templates": { - "target": { - "baseDir": "<%- bin %>", - "manifest": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- platform %>-<%- arch %>", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-<%- platform %>-<%- arch %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %>-<%- platform %>-<%- arch %><%- ext %>", - }, - "vanilla": { - "baseDir": "<%- bin %>", - "manifest": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %>version", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %><%- ext %>", - }, - }, - }, - }, - "userAgent": "@jbrowse/cli/2.11.2 linux-x64 node-v22.2.0", - "userPJSON": undefined, - "valid": true, - "version": "2.11.2", - "warned": false, - "windows": false, - }, - "debug": [Function], - "id": "create", - "token": undefined, - }, - "flags": { - "branch": { - "description": "Download a development build from a named git branch", - "input": [], - "multiple": false, - "name": "branch", - "parse": [Function], - "type": "option", - }, - "force": { - "allowNo": false, - "char": "f", - "description": "Overwrites existing JBrowse 2 installation if present in path", - "name": "force", - "parse": [Function], - "type": "boolean", - }, - "help": { - "allowNo": false, - "char": "h", - "description": "Show CLI help.", - "name": "help", - "parse": [Function], - "type": "boolean", - }, - "listVersions": { - "allowNo": false, - "char": "l", - "description": "Lists out all versions of JBrowse 2", - "name": "listVersions", - "parse": [Function], - "type": "boolean", - }, - "nightly": { - "allowNo": false, - "description": "Download the latest development build from the main branch", - "name": "nightly", - "parse": [Function], - "type": "boolean", - }, - "tag": { - "char": "t", - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "input": [], - "multiple": false, - "name": "tag", - "parse": [Function], - "type": "option", - }, - "url": { - "char": "u", - "description": "A direct URL to a JBrowse 2 release", - "input": [], - "multiple": false, - "name": "url", - "parse": [Function], - "type": "option", - }, - }, - "strict": true, - }, - "output": { - "args": {}, - "argv": [], - "flags": {}, - "metadata": { - "flags": { - "force": { - "setFromDefault": true, - }, - "help": { - "setFromDefault": true, - }, - "listVersions": { - "setFromDefault": true, - }, - "nightly": { - "setFromDefault": true, - }, - }, - }, - "nonExistentFlags": [], - "raw": [], - }, - }, - "showHelp": true, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +See more help with --help" `; exports[`fails if no path is provided to the command, even with force 1`] = ` -{ - "args": [ - { - "description": "Location where JBrowse 2 will be installed", - "input": [], - "name": "localPath", - "parse": [Function], - "required": true, - "type": "option", - }, - ], - "code": undefined, - "message": "Missing 1 required arg: +"Missing 1 required arg: localPath Location where JBrowse 2 will be installed -See more help with --help", - "oclif": { - "exit": 2, - }, - "parse": { - "input": { - "--": undefined, - "args": { - "localPath": { - "description": "Location where JBrowse 2 will be installed", - "input": [], - "name": "localPath", - "parse": [Function], - "required": true, - "type": "option", - }, - }, - "argv": [ - "--force", - ], - "context": Create { - "argv": [ - "--force", - ], - "config": Config { - "_base": "@oclif/core@4.0.6", - "_commandIDs": undefined, - "_commands": Map { - "add-assembly" => { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection" => { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "create" => { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - "", - "# List available versions", - "$ jbrowse create --listVersions", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing JBrowse 2 installation if present in path", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. 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"description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "set-default-session" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - "examples": [ - "$ jbrowse set-default-session --session /path/to/default/session.json", - "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json", - "$ jbrowse set-default-session --view LinearGenomeView, --name newName", - "$ jbrowse set-default-session --currentSession # Prints out current default session", - ], - "flags": { - "currentSession": { - "aliases": undefined, - "allowNo": false, - "char": "c", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "List out the current default session", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "currentSession", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "delete": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Delete any existing default session.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "delete", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": "New Default Session", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff" => { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "upgrade" => { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "help" => { - "aliasPermutations": [], - "aliases": [], - "args": { - "command": { - "description": "Command to show help for.", - "name": "command", - "required": false, - }, - }, - "description": "Display help for <%= config.bin %>.", - "enableJsonFlag": false, - "flags": { - "nested-commands": { - "allowNo": false, - "char": "n", - "description": "Include all nested commands in the output.", - "name": "nested-commands", - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hiddenAliases": [], - "id": "help", - "isESM": true, - "load": [Function], - "permutations": [ - "help", - ], - "pluginAlias": "@oclif/plugin-help", - "pluginName": "@oclif/plugin-help", - "pluginType": "core", - "relativePath": [ - "lib", - "commands", - "help.js", - ], - "strict": false, - }, - }, - "_topics": Map { - "add-assembly" => { - "description": "Add an assembly to a JBrowse 2 configuration", - "name": "add-assembly", - }, - "add-connection" => { - "description": "Add a connection to a JBrowse 2 configuration", - "name": "add-connection", - }, - "add-track" => { - "description": "Add a track to a JBrowse 2 configuration", - "name": "add-track", - }, - "add-track-json" => { - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "name": "add-track-json", - }, - "admin-server" => { - "description": "Start up a small admin server for JBrowse configuration", - "name": "admin-server", - }, - "create" => { - "description": "Downloads and installs the latest JBrowse 2 release", - "name": "create", - }, - "make-pif" => { - "description": "creates pairwise indexed PAF (PIF), with bgzip and tabix", - "name": "make-pif", - }, - "remove-track" => { - "description": "Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!", - "name": "remove-track", - }, - "set-default-session" => { - "description": "Set a default session with views and tracks", - "name": "set-default-session", - }, - "sort-gff" => { - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "name": "sort-gff", - }, - "text-index" => { - "description": "Make a text-indexing file for any given track(s).", - "name": "text-index", - }, - "upgrade" => { - "description": "Upgrades JBrowse 2 to latest version", - "name": "upgrade", - }, - "help" => { - "description": "Display help for <%= config.bin %>.", - "name": "help", - }, - }, - "arch": "x64", - "bin": "jbrowse", - "binAliases": undefined, - "binPath": undefined, - "cacheDir": "/home/cdiesh/.cache/@jbrowse/cli", - "channel": "stable", - "commandPermutations": Map { - "add-assembly" => Set { - "add-assembly", - }, - "add-connection" => Set { - "add-connection", - }, - "add-track" => Set { - "add-track", - }, - "add-track-json" => Set { - "add-track-json", - }, - "admin-server" => Set { - "admin-server", - }, - "create" => Set { - "create", - }, - "make-pif" => Set { - "make-pif", - }, - "remove-track" => Set { - "remove-track", - }, - "set-default-session" => Set { - "set-default-session", - }, - "sort-gff" => Set { - "sort-gff", - }, - "text-index" => Set { - "text-index", - }, - "upgrade" => Set { - "upgrade", - }, - "help" => Set { - "help", - }, - }, - "configDir": "/home/cdiesh/.config/@jbrowse/cli", - "dataDir": "/home/cdiesh/.local/share/@jbrowse/cli", - "dirname": "@jbrowse/cli", - "flexibleTaxonomy": false, - "home": "/home/cdiesh", - "isSingleCommandCLI": false, - "name": "@jbrowse/cli", - "npmRegistry": undefined, - "nsisCustomization": undefined, - "options": { - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - "decompress": "^4.0.0", - "express": "^4.17.1", - "ixixx": "^2.0.1", - "json-parse-better-errors": "^1.0.2", - "node-fetch-native": "^1.6.4", - "rimraf": "^5.0.0", - "tslib": "^2.3.1", - }, - "description": "A command line tool for working with JBrowse 2", - "devDependencies": { - "typescript": "^5.1.3", - }, - "engines": { - "node": ">=16", - }, - "files": [ - "/bin", - "/lib", - "/npm-shrinkwrap.json", - "/oclif.manifest.json", - ], - "homepage": "https://jbrowse.org", - "keywords": [ - "jbrowse", - "jbrowse2", - "oclif", - ], - "license": "Apache-2.0", - "main": "lib/index.js", - "name": "@jbrowse/cli", - "oclif": { - "bin": "jbrowse", - "commands": "./lib/commands", - "plugins": [ - "@oclif/plugin-help", - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>", - }, - "publishConfig": { - "access": "public", - }, - "repository": { - "directory": "products/jbrowse-cli", - "type": "git", - "url": "https://github.com/GMOD/jbrowse-components.git", - }, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "platform": "linux", - "pluginLoader": PluginLoader { - "errors": [], - "options": { - "plugins": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "plugins": Map { - "@jbrowse/cli" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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"hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - 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Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - 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"helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - 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"env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - "", - "# List available versions", - "$ jbrowse create --listVersions", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing JBrowse 2 installation if present in path", - 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"deprecated": undefined, - "description": "Version of JBrowse 2 to install. 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"description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - 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"delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. 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"relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "create": { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "set-default-session": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - "examples": [ - "$ jbrowse set-default-session --session /path/to/default/session.json", - "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json", - "$ jbrowse set-default-session --view LinearGenomeView, --name newName", - "$ jbrowse set-default-session --currentSession # Prints out current default session", - ], - "flags": { - "currentSession": { - "aliases": undefined, - "allowNo": false, - "char": "c", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "List out the current default session", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "currentSession", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "delete": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Delete any existing default session.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "delete", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": "New Default Session", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff": { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. 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"summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - }, - "version": "2.11.2", - }, - "moduleType": "commonjs", - "name": "@jbrowse/cli", - "options": { - "isRoot": true, - "pjson": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "parent": undefined, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - 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}, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli", - "tag": undefined, - "type": "core", - "valid": true, - "version": "2.11.2", - }, - "@oclif/plugin-help" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@oclif/plugin-help", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - 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"rootPlugin": Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - 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Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff": { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. 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"relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - 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"summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. 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If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "upgrade": { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - }, - "version": "2.11.2", - }, - "moduleType": "commonjs", - "name": "@jbrowse/cli", - "options": { - "isRoot": true, - "pjson": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "parent": undefined, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - "decompress": "^4.0.0", - "express": "^4.17.1", - "ixixx": "^2.0.1", - "json-parse-better-errors": "^1.0.2", - "node-fetch-native": "^1.6.4", - "rimraf": "^5.0.0", - "tslib": "^2.3.1", - }, - "description": "A command line tool for working with JBrowse 2", - "devDependencies": { - "typescript": "^5.1.3", - }, - "engines": { - "node": ">=16", - }, - "files": [ - "/bin", - "/lib", - "/npm-shrinkwrap.json", - "/oclif.manifest.json", - ], - "homepage": "https://jbrowse.org", - "keywords": [ - "jbrowse", - "jbrowse2", - "oclif", - ], - "license": "Apache-2.0", - "main": "lib/index.js", - "name": "@jbrowse/cli", - "oclif": { - "bin": "jbrowse", - "commands": "./lib/commands", - "plugins": [ - "@oclif/plugin-help", - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>", - }, - "publishConfig": { - "access": "public", - }, - "repository": { - "directory": "products/jbrowse-cli", - "type": "git", - "url": "https://github.com/GMOD/jbrowse-components.git", - }, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli", - "tag": undefined, - "type": "core", - "valid": true, - "version": "2.11.2", - }, - "shell": "zsh", - "theme": undefined, - "topicPermutations": Map {}, - "topicSeparator": ":", - "updateConfig": { - "node": {}, - "s3": { - "bucket": undefined, - "host": undefined, - "templates": { - "target": { - "baseDir": "<%- bin %>", - "manifest": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- platform %>-<%- arch %>", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-<%- platform %>-<%- arch %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %>-<%- platform %>-<%- arch %><%- ext %>", - }, - "vanilla": { - "baseDir": "<%- bin %>", - "manifest": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %>version", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %><%- ext %>", - }, - }, - }, - }, - "userAgent": "@jbrowse/cli/2.11.2 linux-x64 node-v22.2.0", - "userPJSON": undefined, - "valid": true, - "version": "2.11.2", - "warned": false, - "windows": false, - }, - "debug": [Function], - "id": "create", - "token": undefined, - }, - "flags": { - "branch": { - "description": "Download a development build from a named git branch", - "input": [], - "multiple": false, - "name": "branch", - "parse": [Function], - "type": "option", - }, - "force": { - "allowNo": false, - "char": "f", - "description": "Overwrites existing JBrowse 2 installation if present in path", - "name": "force", - "parse": [Function], - "type": "boolean", - }, - "help": { - "allowNo": false, - "char": "h", - "description": "Show CLI help.", - "name": "help", - "parse": [Function], - "type": "boolean", - }, - "listVersions": { - "allowNo": false, - "char": "l", - "description": "Lists out all versions of JBrowse 2", - "name": "listVersions", - "parse": [Function], - "type": "boolean", - }, - "nightly": { - "allowNo": false, - "description": "Download the latest development build from the main branch", - "name": "nightly", - "parse": [Function], - "type": "boolean", - }, - "tag": { - "char": "t", - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "input": [], - "multiple": false, - "name": "tag", - "parse": [Function], - "type": "option", - }, - "url": { - "char": "u", - "description": "A direct URL to a JBrowse 2 release", - "input": [], - "multiple": false, - "name": "url", - "parse": [Function], - "type": "option", - }, - }, - "strict": true, - }, - "output": { - "args": {}, - "argv": [], - "flags": { - "force": true, - }, - "metadata": { - "flags": { - "help": { - "setFromDefault": true, - }, - "listVersions": { - "setFromDefault": true, - }, - "nightly": { - "setFromDefault": true, - }, - }, - }, - "nonExistentFlags": [], - "raw": [ - { - "flag": "force", - "input": "--force", - "type": "flag", - }, - ], - }, - }, - "showHelp": true, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +See more help with --help" `; -exports[`fails if the fetch does not return the right file 1`] = ` -{ - "code": undefined, - "message": "The URL provided does not seem to be a JBrowse installation URL", - "oclif": { - "exit": 2, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if the fetch does not return the right file 1`] = `"The URL provided does not seem to be a JBrowse installation URL"`; exports[`fails if user selects a directory that already has existing files 1`] = `undefined`; -exports[`fails to download a version that does not exist 1`] = ` -{ - "code": undefined, - "message": "Could not find version: ", - "oclif": { - "exit": 90, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails to download a version that does not exist 1`] = `"Could not find version: "`; diff --git a/products/jbrowse-cli/src/commands/__snapshots__/set-default-session.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/set-default-session.test.ts.snap index cb6956c4b9..42b7973bc4 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/set-default-session.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/set-default-session.test.ts.snap @@ -63,50 +63,10 @@ exports[`deletes a default session 1`] = ` } `; -exports[`fails when default session is not readable 1`] = ` -{ - "code": undefined, - "message": "Could not read the provided file", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails when default session is not readable 1`] = `"Could not read the provided file"`; -exports[`fails when file does not exist 1`] = ` -{ - "code": undefined, - "message": "Could not read the provided file", - "oclif": { - "exit": 150, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails when file does not exist 1`] = `"Could not read the provided file"`; -exports[`fails when file is does not have a default session to read 1`] = ` -{ - "code": undefined, - "message": "Could not parse the given default session file", - "oclif": { - "exit": 160, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails when file is does not have a default session to read 1`] = `"Could not parse the given default session file"`; -exports[`fails when no necessary default session information is provided 1`] = ` -{ - "code": undefined, - "message": "Please either provide a default session file", - "oclif": { - "exit": 120, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails when no necessary default session information is provided 1`] = `"Please either provide a default session file"`; diff --git a/products/jbrowse-cli/src/commands/__snapshots__/text-index.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/text-index.test.ts.snap index 258f9fe644..fcba88c61e 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/text-index.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/text-index.test.ts.snap @@ -1,21359 +1,10 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`fails if no track ids are provided with --tracks flag. 1`] = ` -{ - "code": undefined, - "message": "Flag --tracks expects a value", - "oclif": { - "exit": 2, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} -`; +exports[`fails if no track ids are provided with --tracks flag. 1`] = `"Flag --tracks expects a value"`; exports[`fails if there is an invalid flag 1`] = ` -{ - "code": undefined, - "flags": [ - "--Command", - ], - "message": "Nonexistent flag: --Command -See more help with --help", - "oclif": { - "exit": 2, - }, - "parse": { - "input": { - "--": undefined, - "args": {}, - "argv": [ - "--Command", - ], - "context": TextIndex { - "argv": [ - "--Command", - ], - "config": Config { - "_base": "@oclif/core@4.0.6", - "_commandIDs": undefined, - "_commands": Map { - "add-assembly" => { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection" => { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json" => { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "create" => { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - "", - "# List available versions", - "$ jbrowse create --listVersions", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing JBrowse 2 installation if present in path", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. 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"description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "set-default-session" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - "examples": [ - "$ jbrowse set-default-session --session /path/to/default/session.json", - "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json", - "$ jbrowse set-default-session --view LinearGenomeView, --name newName", - "$ jbrowse set-default-session --currentSession # Prints out current default session", - ], - "flags": { - "currentSession": { - "aliases": undefined, - "allowNo": false, - "char": "c", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "List out the current default session", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "currentSession", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "delete": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Delete any existing default session.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "delete", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": "New Default Session", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff" => { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index" => { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "upgrade" => { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "help" => { - "aliasPermutations": [], - "aliases": [], - "args": { - "command": { - "description": "Command to show help for.", - "name": "command", - "required": false, - }, - }, - "description": "Display help for <%= config.bin %>.", - "enableJsonFlag": false, - "flags": { - "nested-commands": { - "allowNo": false, - "char": "n", - "description": "Include all nested commands in the output.", - "name": "nested-commands", - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hiddenAliases": [], - "id": "help", - "isESM": true, - "load": [Function], - "permutations": [ - "help", - ], - "pluginAlias": "@oclif/plugin-help", - "pluginName": "@oclif/plugin-help", - "pluginType": "core", - "relativePath": [ - "lib", - "commands", - "help.js", - ], - "strict": false, - }, - }, - "_topics": Map { - "add-assembly" => { - "description": "Add an assembly to a JBrowse 2 configuration", - "name": "add-assembly", - }, - "add-connection" => { - "description": "Add a connection to a JBrowse 2 configuration", - "name": "add-connection", - }, - "add-track" => { - "description": "Add a track to a JBrowse 2 configuration", - "name": "add-track", - }, - "add-track-json" => { - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "name": "add-track-json", - }, - "admin-server" => { - "description": "Start up a small admin server for JBrowse configuration", - "name": "admin-server", - }, - "create" => { - "description": "Downloads and installs the latest JBrowse 2 release", - "name": "create", - }, - "make-pif" => { - "description": "creates pairwise indexed PAF (PIF), with bgzip and tabix", - "name": "make-pif", - }, - "remove-track" => { - "description": "Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!", - "name": "remove-track", - }, - "set-default-session" => { - "description": "Set a default session with views and tracks", - "name": "set-default-session", - }, - "sort-gff" => { - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "name": "sort-gff", - }, - "text-index" => { - "description": "Make a text-indexing file for any given track(s).", - "name": "text-index", - }, - "upgrade" => { - "description": "Upgrades JBrowse 2 to latest version", - "name": "upgrade", - }, - "help" => { - "description": "Display help for <%= config.bin %>.", - "name": "help", - }, - }, - "arch": "x64", - "bin": "jbrowse", - "binAliases": undefined, - "binPath": undefined, - "cacheDir": "/home/cdiesh/.cache/@jbrowse/cli", - "channel": "stable", - "commandPermutations": Map { - "add-assembly" => Set { - "add-assembly", - }, - "add-connection" => Set { - "add-connection", - }, - "add-track" => Set { - "add-track", - }, - "add-track-json" => Set { - "add-track-json", - }, - "admin-server" => Set { - "admin-server", - }, - "create" => Set { - "create", - }, - "make-pif" => Set { - "make-pif", - }, - "remove-track" => Set { - "remove-track", - }, - "set-default-session" => Set { - "set-default-session", - }, - "sort-gff" => Set { - "sort-gff", - }, - "text-index" => Set { - "text-index", - }, - "upgrade" => Set { - "upgrade", - }, - "help" => Set { - "help", - }, - }, - "configDir": "/home/cdiesh/.config/@jbrowse/cli", - "dataDir": "/home/cdiesh/.local/share/@jbrowse/cli", - "dirname": "@jbrowse/cli", - "flexibleTaxonomy": false, - "home": "/home/cdiesh", - "isSingleCommandCLI": false, - "name": "@jbrowse/cli", - "npmRegistry": undefined, - "nsisCustomization": undefined, - "options": { - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - "decompress": "^4.0.0", - "express": "^4.17.1", - "ixixx": "^2.0.1", - "json-parse-better-errors": "^1.0.2", - "node-fetch-native": "^1.6.4", - "rimraf": "^5.0.0", - "tslib": "^2.3.1", - }, - "description": "A command line tool for working with JBrowse 2", - "devDependencies": { - "typescript": "^5.1.3", - }, - "engines": { - "node": ">=16", - }, - "files": [ - "/bin", - "/lib", - "/npm-shrinkwrap.json", - "/oclif.manifest.json", - ], - "homepage": "https://jbrowse.org", - "keywords": [ - "jbrowse", - "jbrowse2", - "oclif", - ], - "license": "Apache-2.0", - "main": "lib/index.js", - "name": "@jbrowse/cli", - "oclif": { - "bin": "jbrowse", - "commands": "./lib/commands", - "plugins": [ - "@oclif/plugin-help", - ], - "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>", - }, - "publishConfig": { - "access": "public", - }, - "repository": { - "directory": "products/jbrowse-cli", - "type": "git", - "url": "https://github.com/GMOD/jbrowse-components.git", - }, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "platform": "linux", - "pluginLoader": PluginLoader { - "errors": [], - "options": { - "plugins": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "plugins": Map { - "@jbrowse/cli" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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"hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - 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Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - 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"helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - 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"env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - "", - "# List available versions", - "$ jbrowse create --listVersions", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing JBrowse 2 installation if present in path", - 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"deprecated": undefined, - "description": "Version of JBrowse 2 to install. 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"description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - 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"delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. 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"relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "trackId for the track, by default inferred from filename, must be unique throughout config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "trackType": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of track, by default inferred from track file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "trackType", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track-json": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "track JSON file or command line arg blob", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-track-json track.json", - "$ jbrowse add-track-json track.json --update", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "update": { - "aliases": undefined, - "allowNo": false, - "char": "u", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "update the contents of an existing track, matched based on trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "update", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-track-json", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-track-json.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "admin-server": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Start up a small admin server for JBrowse configuration", - "examples": [ - "$ jbrowse admin-server", - "$ jbrowse admin-server -p 8888", - ], - "flags": { - "bodySizeLimit": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "25mb", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Size limit of the update message; may need to increase if config is large. -Argument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bodySizeLimit", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "port": { - "aliases": undefined, - "char": "p", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specifified port to start the server on; -Default is 9090.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "port", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "root": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to the root of the JB2 installation. -Creates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "root", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "admin-server", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "admin-server.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "create": { - "aliases": [], - "args": { - "localPath": { - "default": undefined, - "description": "Location where JBrowse 2 will be installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Downloads and installs the latest JBrowse 2 release", - "examples": [ - "# Download latest release from github, and put in specific path", - "$ jbrowse create /path/to/new/installation", - "", - "# Download latest release from github and force overwrite existing contents at path", - "$ jbrowse create /path/to/new/installation --force", - "", - "# Download latest release from a specific URL", - "$ jbrowse create /path/to/new/installation --url url.com/directjbrowselink.zip", - "", - "# Download a specific tag from github", - "$ jbrowse create /path/to/new/installation --tag v1.0.0", - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "remove-track", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "remove-track.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "set-default-session": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Set a default session with views and tracks", - "examples": [ - "$ jbrowse set-default-session --session /path/to/default/session.json", - "$ jbrowse set-default-session --target /path/to/jb2/installation/config.json", - "$ jbrowse set-default-session --view LinearGenomeView, --name newName", - "$ jbrowse set-default-session --currentSession # Prints out current default session", - ], - "flags": { - "currentSession": { - "aliases": undefined, - "allowNo": false, - "char": "c", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "List out the current default session", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "currentSession", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "delete": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Delete any existing default session.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "delete", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": "New Default Session", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Give a name for the default session", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "session": { - "aliases": undefined, - "char": "s", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "set path to a file containing session in json format", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "session", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "sort-gff": { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. 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"summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - }, - "version": "2.11.2", - }, - "moduleType": "commonjs", - "name": "@jbrowse/cli", - "options": { - "isRoot": true, - "pjson": undefined, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - }, - "parent": undefined, - "pjson": { - "author": "JBrowse Team", - "bin": { - "jbrowse": "./bin/run", - }, - "bugs": "https://github.com/GMOD/jbrowse-components/issues", - "dependencies": { - "@oclif/core": "^4.0.6", - "@oclif/plugin-help": "^6.0.15", - "boxen": "^4.2.0", - "chalk": "^4.1.0", - "cli-progress": "^3.9.0", - "command-exists": "^1.2.9", - "cors": "^2.8.5", - 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}, - "scripts": { - "build": "tsc --build", - "clean": "rimraf lib", - "docs": "npm run docs:create && npm run docs:format", - "docs:create": "oclif readme", - "docs:format": "prettier --write README.md", - "docs:version:add": "git add README.md", - "manifest": "oclif manifest", - "postpack": "rimraf oclif.manifest.json", - "prebuild": "npm run clean", - "predocs": "npm run build", - "prepack": "npm run clean && npm run build && npm run manifest && npm run docs", - "version": "npm run docs && npm run docs:version:add", - }, - "types": "lib/index.d.ts", - "version": "2.11.2", - }, - "root": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli", - "tag": undefined, - "type": "core", - "valid": true, - "version": "2.11.2", - }, - "@oclif/plugin-help" => Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@oclif/plugin-help", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - 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"rootPlugin": Plugin { - "_base": "@oclif/core@4.0.6", - "_debug": [Function], - "alias": "@jbrowse/cli", - "alreadyLoaded": false, - "children": [], - "commandCache": undefined, - "commandDiscoveryOpts": { - "globPatterns": [ - "**/*.+(js|cjs|mjs|ts|tsx|mts|cts)", - "!**/*.+(d.ts|test.ts|test.js|spec.ts|spec.js|d.mts|d.cts)?(x)", - ], - "strategy": "pattern", - "target": "./lib/commands", - }, - "commandIDs": [ - "add-assembly", - "add-connection", - "add-track-json", - "add-track", - "admin-server-test-utils", - "admin-server", - "create", - "make-pif", - "remove-track", - "set-default-session", - "sort-gff", - "text-index", - "upgrade", - ], - "commands": [ - { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - 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Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "when using --load a file, output to a subdirectory of the target dir", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "subDir", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - 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"deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "set-default-session", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "set-default-session.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "file": { - "default": undefined, - "description": "GFF file", - "hidden": undefined, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblies", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "attributes": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "Name,ID", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Comma separated list of attributes to index", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "attributes", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "dryrun": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "dryrun", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "exclude": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "CDS,exon", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Adds gene type to list of excluded types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "exclude", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "file": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "file", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "fileId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Set the trackId used for the indexes generated with the --file argument", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "fileId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite previously existing indexes", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "perTrack": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "If set, creates an index per track", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "perTrack", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "prefixSize": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "prefixSize", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "quiet": { - "aliases": undefined, - "allowNo": false, - "char": "q", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Hide the progress bars", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "quiet", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Path to config file in JB2 installation directory to read from.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "tracks": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tracks", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "text-index", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "text-index.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - { - "aliases": [], - "args": { - "localPath": { - "default": ".", - "description": "Location where JBrowse 2 is installed", - "hidden": undefined, - "name": "localPath", - "noCacheDefault": undefined, - "options": undefined, - "required": false, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Upgrades JBrowse 2 to latest version", - "examples": [ - "# Upgrades current directory to latest jbrowse release", - "$ jbrowse upgrade", - "", - "# Upgrade jbrowse instance at a specific filesystem path", - "$ jbrowse upgrade /path/to/jbrowse2/installation", - "", - "# Upgrade to a specific tag", - "$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0", - "", - "# List versions available on github", - "$ jbrowse upgrade --listVersions", - "", - "# Upgrade from a specific URL", - "$ jbrowse upgrade --url https://sample.com/jbrowse2.zip", - "", - "# Get nightly release from main branch", - "$ jbrowse upgrade --nightly", - ], - "flags": { - "branch": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download a development build from a named git branch", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "branch", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "clean": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Removes old js,map,and LICENSE files in the installation", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "clean", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "listVersions": { - "aliases": undefined, - "allowNo": false, - "char": "l", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Lists out all versions of JBrowse 2", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "listVersions", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "nightly": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Download the latest development build from the main branch", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "nightly", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "tag": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Version of JBrowse 2 to install. Format is v1.0.0. -Defaults to latest", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "tag", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "url": { - "aliases": undefined, - "char": "u", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A direct URL to a JBrowse 2 release", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "url", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "upgrade", - "isESM": false, - "load": [Function], - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "upgrade.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - ], - "commandsDir": "/home/cdiesh/src/jbrowse-components/products/jbrowse-cli/src/commands", - "flexibleTaxonomy": false, - "hasManifest": false, - "hooks": {}, - "isRoot": true, - "manifest": { - "commands": { - "add-assembly": { - "aliases": [], - "args": { - "sequence": { - "default": undefined, - "description": "sequence file or URL - -If TYPE is indexedFasta or bgzipFasta, the index file defaults to .fai -and can be optionally specified with --faiLocation -If TYPE is bgzipFasta, the gzip index file defaults to .gzi and can be -optionally specified with --gziLocation", - "hidden": undefined, - "name": "sequence", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add an assembly to a JBrowse 2 configuration", - "examples": [ - "# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory", - "$ jbrowse add-assembly GRCh38.fa --load copy", - "", - "# add assembly to a specific jb2 installation path using --out, and copies the .fa and .fa.fai file to /path/to/jb2", - "$ jbrowse add-assembly GRCh38.fa --out /path/to/jb2/ --load copy", - "", - "# force indexedFasta for add-assembly without relying on file extension", - "$ jbrowse add-assembly GRCh38.xyz --type indexedFasta --load copy", - "", - "# add displayName for an assembly", - "$ jbrowse add-assembly myFile.fa.gz --name hg38 --displayName "Homo sapiens (hg38)"", - "", - "# use chrom.sizes file for assembly instead of a fasta file", - "$ jbrowse add-assembly GRCh38.chrom.sizes --load inPlace", - "", - "# add assembly from preconfigured json file, expert option", - "$ jbrowse add-assembly GRCh38.config.json --load copy", - "", - "# add assembly from a 2bit file, also note pointing direct to a URL so no --load flag needed", - "$ jbrowse add-assembly https://example.com/data/sample.2bit", - "", - "# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists", - "$ jbrowse add-assembly myfile.fa.gz --load copy", - ], - "flags": { - "alias": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); -can be specified multiple times", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": true, - "name": "alias", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "displayName": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "displayName", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "faiLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .fai] FASTA index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "faiLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "gziLocation": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "[default: .gzi] FASTA gzip index file or URL", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "gziLocation", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the assembly; if not specified, will be guessed using the sequence file name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrite existing assembly if one with the same name exists", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "refNameAliases": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Reference sequence name aliases file or URL; assumed to be a tab-separated aliases -file unless --refNameAliasesType is specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliases", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameAliasesType": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": [ - "refNameAliases", - ], - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either -a JSON file location or inline JSON that defines a custom sequence adapter", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameAliasesType", - "noCacheDefault": undefined, - "options": [ - "aliases", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "refNameColors": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "A comma-separated list of color strings for the reference sequence names; will cycle -through colors if there are fewer colors than sequences", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "refNameColors", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to. -Creates ./config.json if nonexistent", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of sequence, by default inferred from sequence file - -indexedFasta An index FASTA (e.g. .fa or .fasta) file; - can optionally specify --faiLocation - -bgzipFasta A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; - can optionally specify --faiLocation and/or --gziLocation - -twoBit A twoBit (e.g. .2bit) file - -chromSizes A chromosome sizes (e.g. .chrom.sizes) file - -custom Either a JSON file location or inline JSON that defines a custom - sequence adapter; must provide --name if using inline JSON", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": [ - "indexedFasta", - "bgzipFasta", - "twoBit", - "chromSizes", - "custom", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-assembly", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-assembly.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-connection": { - "aliases": [], - "args": { - "connectionUrlOrPath": { - "default": undefined, - "description": "URL of data directory -For hub file, usually called hub.txt -For JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ", - "hidden": undefined, - "name": "connectionUrlOrPath", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a connection to a JBrowse 2 configuration", - "examples": [ - "$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19", - "$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38", - "$ jbrowse add-connection http://mysite.com/path/to/hub.txt", - "$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection", - "$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19", - "$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": "c", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "connectionId": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Id for the connection that must be unique to JBrowse. Defaults to 'connectionType-assemblyName-currentTime'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "connectionId", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the connection. Defaults to connectionId if not provided", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites any existing connections if same connection id", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "path to config file in JB2 installation directory to write out to.", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "target", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "type": { - "aliases": undefined, - "char": "t", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "type", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "add-connection", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "add-connection.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "add-track": { - "aliases": [], - "args": { - "track": { - "default": undefined, - "description": "Track file or URL", - "hidden": undefined, - "name": "track", - "noCacheDefault": undefined, - "options": undefined, - "required": true, - }, - }, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Add a track to a JBrowse 2 configuration", - "examples": [ - "# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load copy", - "", - "# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json", - "$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam", - "", - "# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai", - "$ jbrowse add-track my.bam --indexFile my.bai --load copy", - "", - "# creates symlink for /path/to/my.bam and adds track to config.json", - "$ jbrowse add-track /path/to/my.bam --load symlink", - "", - "# add track from URL to config.json, no --load flag needed", - "$ jbrowse add-track https://mywebsite.com/my.bam", - "", - "# --load inPlace adds a track without doing file operations", - "$ jbrowse add-track /url/relative/path.bam --load inPlace", - ], - "flags": { - "assemblyNames": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "assemblyNames", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed1": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed1", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "bed2": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Used only for mcscan anchors/simpleAnchors types", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "bed2", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "category": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional Comma separated string of categories to group tracks", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "category", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "config": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "config", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "description": { - "aliases": undefined, - "char": "d", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional description of the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "description", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "force": { - "aliases": undefined, - "allowNo": false, - "char": "f", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Equivalent to \`--skipCheck --overwrite\`", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "force", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "indexFile": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Optional index file for the track", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "indexFile", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "load": { - "aliases": undefined, - "char": "l", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "load", - "noCacheDefault": undefined, - "options": [ - "copy", - "symlink", - "move", - "inPlace", - ], - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "name": { - "aliases": undefined, - "char": "n", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Name of the track. Will be defaulted to the trackId if none specified", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "name", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "overwrite": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Overwrites existing track if it shares the same trackId", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "overwrite", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "protocol": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "uri", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Force protocol to a specific value", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "protocol", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "skipCheck": { - "aliases": undefined, - "allowNo": false, - "char": undefined, - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Skip check for whether or not the file or URL exists or if you are in a JBrowse directory", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "skipCheck", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - "subDir": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": "", - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - 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Be aware that this can cause crashes in saved sessions that refer to this track!", - "examples": [ - "$ jbrowse remove-track-json trackId", - ], - "flags": { - "out": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "synonym for target", - "env": undefined, - "exclusive": undefined, - "hasDynamicHelp": false, - "helpGroup": undefined, - "helpLabel": undefined, - "helpValue": undefined, - "hidden": undefined, - "multiple": false, - "name": "out", - "noCacheDefault": undefined, - "options": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "option", - }, - "target": { - "aliases": undefined, - "char": undefined, - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - 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Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep", - "examples": [ - "# sort gff and pipe to bgzip", - "$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz", - "$ tabix sorted.gff.gz", - ], - "flags": { - "help": { - "aliases": undefined, - "allowNo": false, - "char": "h", - "charAliases": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Show CLI help.", - "env": undefined, - "exclusive": undefined, - "helpGroup": undefined, - "helpLabel": undefined, - "hidden": undefined, - "name": "help", - "noCacheDefault": undefined, - "relationships": undefined, - "required": undefined, - "summary": undefined, - "type": "boolean", - }, - }, - "hasDynamicHelp": false, - "hidden": undefined, - "hiddenAliases": [], - "id": "sort-gff", - "isESM": false, - "pluginAlias": "@jbrowse/cli", - "pluginName": "@jbrowse/cli", - "pluginType": "core", - "relativePath": [ - "src", - "commands", - "sort-gff.ts", - ], - "state": undefined, - "strict": true, - "summary": undefined, - "usage": undefined, - }, - "text-index": { - "aliases": [], - "args": {}, - "deprecateAliases": undefined, - "deprecationOptions": undefined, - "description": "Make a text-indexing file for any given track(s).", - "examples": [ - "# indexes all tracks that it can find in the current directory's config.json", - "$ jbrowse text-index", - "", - "# indexes specific trackIds that it can find in the current directory's config.json", - "$ jbrowse text-index --tracks=track1,track2,track3", - "", - "# indexes all tracks in a directory's config.json or in a specific config file", - "$ jbrowse text-index --out /path/to/jb2/", - "", - "# indexes only a specific assembly, and overwrite what was previously there using force (which is needed if a previous index already existed)", - "$ jbrowse text-index -a hg19 --force", - "", - "# create index for some files for use in @jbrowse/react-linear-genome-view or similar", - "$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes", - ], - "flags": { - "assemblies": { - "aliases": undefined, - "char": "a", - "charAliases": undefined, - "default": undefined, - "delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the assembl(ies) to create an index for. 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"delimiter": undefined, - "dependsOn": undefined, - "deprecateAliases": undefined, - "deprecated": undefined, - "description": "Specify the prefix size for the ixx index. 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'' : 'channels/' + channel + '/' %><%- platform %>-<%- arch %>", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-<%- platform %>-<%- arch %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %>-<%- platform %>-<%- arch %><%- ext %>", - }, - "vanilla": { - "baseDir": "<%- bin %>", - "manifest": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %>version", - "unversioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %><%- ext %>", - "versioned": "<%- channel === 'stable' ? '' : 'channels/' + channel + '/' %><%- bin %>-v<%- version %>/<%- bin %>-v<%- version %><%- ext %>", - }, - }, - }, - }, - "userAgent": "@jbrowse/cli/2.11.2 linux-x64 node-v22.2.0", - "userPJSON": undefined, - "valid": true, - "version": "2.11.2", - "warned": false, - "windows": false, - }, - "debug": [Function], - "id": "text-index", - }, - "flags": { - "assemblies": { - "char": "a", - "description": "Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config", - "input": [], - "multiple": false, - "name": "assemblies", - "parse": [Function], - "type": "option", - }, - "attributes": { - "default": "Name,ID", - "description": "Comma separated list of attributes to index", - "input": [], - "multiple": false, - "name": "attributes", - "parse": [Function], - "type": "option", - }, - "dryrun": { - "allowNo": false, - "description": "Just print out tracks that will be indexed by the process, without doing any indexing", - "name": "dryrun", - "parse": [Function], - "type": "boolean", - }, - "exclude": { - "default": "CDS,exon", - "description": "Adds gene type to list of excluded types", - "input": [], - "multiple": false, - "name": "exclude", - "parse": [Function], - "type": "option", - }, - "file": { - "description": "File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)", - "input": [], - "multiple": true, - "name": "file", - "parse": [Function], - "type": "option", - }, - "fileId": { - "description": "Set the trackId used for the indexes generated with the --file argument", - "input": [], - "multiple": true, - "name": "fileId", - "parse": [Function], - "type": "option", - }, - "force": { - "allowNo": false, - "default": false, - "description": "Overwrite previously existing indexes", - "name": "force", - "parse": [Function], - "type": "boolean", - }, - "help": { - "allowNo": false, - "char": "h", - "description": "Show CLI help.", - "name": "help", - "parse": [Function], - "type": "boolean", - }, - "out": { - "description": "Synonym for target", - "input": [], - "multiple": false, - "name": "out", - "parse": [Function], - "type": "option", - }, - "perTrack": { - "allowNo": false, - "default": false, - "description": "If set, creates an index per track", - "name": "perTrack", - "parse": [Function], - "type": "boolean", - }, - "prefixSize": { - "description": "Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins", - "input": [], - "multiple": false, - "name": "prefixSize", - "parse": [Function], - "type": "option", - }, - "quiet": { - "allowNo": false, - "char": "q", - "default": false, - "description": "Hide the progress bars", - "name": "quiet", - "parse": [Function], - "type": "boolean", - }, - "target": { - "description": "Path to config file in JB2 installation directory to read from.", - "input": [], - "multiple": false, - "name": "target", - "parse": [Function], - "type": "option", - }, - "tracks": { - "description": "Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks", - "input": [], - "multiple": false, - "name": "tracks", - "parse": [Function], - "type": "option", - }, - }, - "strict": true, - }, - "output": { - "args": {}, - "argv": [ - "--Command", - ], - "flags": { - "attributes": "Name,ID", - "exclude": "CDS,exon", - "force": false, - "perTrack": false, - "quiet": false, - }, - "metadata": { - "flags": { - "attributes": { - "setFromDefault": true, - }, - "dryrun": { - "setFromDefault": true, - }, - "exclude": { - "setFromDefault": true, - }, - "force": { - "setFromDefault": true, - }, - "help": { - "setFromDefault": true, - }, - "perTrack": { - "setFromDefault": true, - }, - "quiet": { - "setFromDefault": true, - }, - }, - }, - "nonExistentFlags": [ - "--Command", - ], - "raw": [], - }, - }, - "showHelp": true, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"Nonexistent flag: --Command +See more help with --help" `; exports[`indexes a local gz gff3 file 1`] = ` diff --git a/products/jbrowse-cli/src/commands/__snapshots__/upgrade.test.ts.snap b/products/jbrowse-cli/src/commands/__snapshots__/upgrade.test.ts.snap index 13e96077d0..f1d78eccaa 100644 --- a/products/jbrowse-cli/src/commands/__snapshots__/upgrade.test.ts.snap +++ b/products/jbrowse-cli/src/commands/__snapshots__/upgrade.test.ts.snap @@ -1,53 +1,21 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP exports[`fails if the fetch does not return the right file 1`] = ` -{ - "code": undefined, - "message": "No manifest.json found in this directory, are you sure it is an - existing jbrowse 2 installation?", - "oclif": { - "exit": 10, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"No manifest.json found in this directory, are you sure it is an + existing jbrowse 2 installation?" `; exports[`fails if user selects a directory that does not exist 1`] = ` -{ - "code": undefined, - "message": "No manifest.json found in this directory, are you sure it is an - existing jbrowse 2 installation?", - "oclif": { - "exit": 10, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"No manifest.json found in this directory, are you sure it is an + existing jbrowse 2 installation?" `; exports[`fails if user selects a directory that does not have a installation 1`] = ` -{ - "code": undefined, - "message": "No manifest.json found in this directory, are you sure it is an - existing jbrowse 2 installation?", - "oclif": { - "exit": 10, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"No manifest.json found in this directory, are you sure it is an + existing jbrowse 2 installation?" `; exports[`fails to upgrade if version does not exist 1`] = ` -{ - "code": undefined, - "message": "No manifest.json found in this directory, are you sure it is an - existing jbrowse 2 installation?", - "oclif": { - "exit": 10, - }, - "skipOclifErrorHandling": undefined, - "suggestions": undefined, -} +"No manifest.json found in this directory, are you sure it is an + existing jbrowse 2 installation?" `; diff --git a/products/jbrowse-cli/src/commands/add-assembly.test.ts b/products/jbrowse-cli/src/commands/add-assembly.test.ts index e1f0a6ec5a..f64b8a59ae 100644 --- a/products/jbrowse-cli/src/commands/add-assembly.test.ts +++ b/products/jbrowse-cli/src/commands/add-assembly.test.ts @@ -22,12 +22,12 @@ afterAll(() => (process.exitCode = 0)) test('add-assembly no load flag', async () => { const { error } = await runCommand('add-assembly {}') - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if using inline JSON sequence custom with no --name', async () => { const { error } = await runCommand(['add-assembly', '{}', '--load', 'copy']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if custom sequence adapter has no type', async () => { const { error } = await runCommand([ @@ -38,7 +38,7 @@ test('fails if custom sequence adapter has no type', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if custom refNameAliases adapter has no type', async () => { const { error } = await runCommand([ @@ -53,7 +53,7 @@ test('fails if custom refNameAliases adapter has no type', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if custom refNameAliases adapter has no type', async () => { const { error } = await runCommand([ @@ -68,7 +68,7 @@ test('fails if custom refNameAliases adapter has no type', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if trying to add an assembly with a name that already exists', async () => { @@ -84,7 +84,7 @@ test('fails if trying to add an assembly with a name that already exists', async await copyFile(simple2bit, path.join(ctx.dir, path.basename(simple2bit))) await runCommand('add-assembly simple.2bit --load copy') const { error } = await runCommand('add-assembly simple.2bit --load copy') - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if it cannot guess the sequence type', async () => { @@ -94,7 +94,7 @@ test('fails if it cannot guess the sequence type', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if it cannot find a file', async () => { @@ -104,7 +104,7 @@ test('fails if it cannot find a file', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if using invalid inline JSON', async () => { @@ -120,7 +120,7 @@ test('fails if using invalid inline JSON', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if load flag is passed with a URL', async () => { @@ -130,7 +130,7 @@ test('fails if load flag is passed with a URL', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('adds an assembly from a FASTA', async () => { diff --git a/products/jbrowse-cli/src/commands/add-connection.test.ts b/products/jbrowse-cli/src/commands/add-connection.test.ts index 724b29a3fb..4d999d0812 100644 --- a/products/jbrowse-cli/src/commands/add-connection.test.ts +++ b/products/jbrowse-cli/src/commands/add-connection.test.ts @@ -5,37 +5,12 @@ import fs from 'fs' import path from 'path' -import { setup, readConf, runInTmpDir } from '../testUtil' +import { readConf, runInTmpDir } from '../testUtil' import nock from 'nock' import { runCommand } from '@oclif/test' const { copyFile, rename } = fs.promises -const defaultConfig = { - assemblies: [ - { - name: 'testAssembly', - sequence: { - type: 'testSequenceTrack', - trackId: '', - adapter: { - type: 'testSeqAdapter', - twoBitLocation: { - uri: 'test.2bit', - locationType: 'UriLocation', - }, - }, - }, - }, - ], - configuration: {}, - connections: [], - defaultSession: { - name: 'New Session', - }, - tracks: [], -} - const testConfig = path.join( __dirname, '..', @@ -53,17 +28,9 @@ async function copyConf(ctx: { dir: string }) { path.join(ctx.dir, 'config.json'), ) } -// const originalDateNow = Date.now - -// const setupWithDateMock = setup -// .do(() => { -// Date.now = jest.fn(() => 1) -// }) -// .finally(() => { -// Date.now = originalDateNow -// }) -// Cleaning up exitCode in Node.js 20, xref https://github.com/jestjs/jest/issues/14501 +// Cleaning up exitCode in Node.js 20, xref +// https://github.com/jestjs/jest/issues/14501 afterAll(() => (process.exitCode = 0)) beforeAll(() => (Date.now = jest.fn(() => 1))) @@ -71,22 +38,24 @@ test('fails if no config file', async () => { nock('https://example.com').head('/hub.txt').reply(200) const { error } = await runCommand([ - 'add-connection https://example.com/hub.txt', + 'add-connection', + 'https://example.com/hub.txt', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if data directory is not an url', async () => { const { error } = await runCommand(['add-connection .']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails when fetching from url fails', async () => { nock('https://mysite.com').head('/notafile.txt').reply(500) const { error } = await runCommand([ - 'add-connection https://mysite.com/notafile.txt', + 'add-connection', + 'https://mysite.com/notafile.txt', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('adds an UCSCTrackHubConnection connection from a url', async () => { @@ -94,7 +63,7 @@ test('adds an UCSCTrackHubConnection connection from a url', async () => { nock('https://mysite.com').head('/data/hub.txt').reply(200) await copyConf(ctx) await runCommand(['add-connection', 'https://mysite.com/data/hub.txt']) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).connections).toMatchSnapshot() }) }) @@ -103,7 +72,7 @@ test('adds JBrowse1 connection from a url', async () => { nock('https://mysite.com').head('/jbrowse/data').reply(200) await copyConf(ctx) await runCommand(['add-connection', 'https://mysite.com/jbrowse/data']) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).connections).toMatchSnapshot() }) }) test('adds a custom connection with user set fields', async () => { @@ -124,7 +93,7 @@ test('adds a custom connection with user set fields', async () => { '--config', '{"url":{"uri":"https://mysite.com/custom"},"locationType":"UriLocation"}', ]) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).connections).toMatchSnapshot() }) }) test('fails to add a duplicate connection', async () => { @@ -148,7 +117,7 @@ test('fails to add a duplicate connection', async () => { '--config', '{"url":{"uri":"https://mysite.com/custom"},"locationType":"UriLocation"}', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('overwrites an existing custom connection and does not check URL', async () => { @@ -174,6 +143,6 @@ test('overwrites an existing custom connection and does not check URL', async () '{"url":{"uri":"https://mysite.com/custom"},"locationType":"UriLocation"}', '--force', ]) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).connections).toMatchSnapshot() }) }) diff --git a/products/jbrowse-cli/src/commands/add-track.test.ts b/products/jbrowse-cli/src/commands/add-track.test.ts index 2fe9311685..84efdcaa2a 100644 --- a/products/jbrowse-cli/src/commands/add-track.test.ts +++ b/products/jbrowse-cli/src/commands/add-track.test.ts @@ -52,7 +52,7 @@ test('fails if no track is specified', async () => { test('fails if load flag is not passed in for a localFile', async () => { const { error } = await runCommand(['add-track', simpleBam]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if URL with load flag is passed', async () => { @@ -62,7 +62,7 @@ test('fails if URL with load flag is passed', async () => { '--load', 'inPlace', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('cannot add a track with the same track id', async () => { @@ -75,7 +75,7 @@ test('cannot add a track with the same track id', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -131,7 +131,7 @@ test('cannot add a track if there is no config file', async () => { '--load', 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if it cannot assume the assemblyname', async () => { @@ -145,7 +145,7 @@ test('fails if it cannot assume the assemblyname', async () => { 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -155,7 +155,7 @@ test('adds a bam track with bai', async () => { await runCommand(['add-track', simpleBam, '--load', 'copy']) expect(exists(path.join(ctx.dir, 'simple.bam'))).toBeTruthy() expect(exists(path.join(ctx.dir, 'simple.bam.bai'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -172,7 +172,7 @@ test('adds a bam track with csi', async () => { ]) expect(exists(path.join(ctx.dir, 'simple.bam'))).toBeTruthy() expect(exists(path.join(ctx.dir, 'simple.bam.csi'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -185,7 +185,7 @@ test('adds a bam track with load inPlace', async () => { '--load', 'inPlace', ]) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -200,7 +200,7 @@ test('adds a bam+bai track with load inPlace', async () => { '--indexFile', '/something/else/random.bai', ]) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -217,7 +217,7 @@ test('adds a bam track with indexFile for bai', async () => { ]) expect(exists(ctxDir(ctx, 'simple.bam'))).toBeTruthy() expect(exists(ctxDir(ctx, 'simple.bai'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -235,7 +235,7 @@ test('adds a bam track with subDir', async () => { expect(exists(ctxDir(ctx, 'bam/simple.bam'))).toBeTruthy() expect(exists(ctxDir(ctx, 'bam/simple.bam.bai'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -256,7 +256,7 @@ test('adds a bam track with subDir and localPath protocol', async () => { expect(exists(ctxDir(ctx, 'bam/simple.bam'))).toBeTruthy() expect(exists(ctxDir(ctx, 'bam/simple.bam.bai'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -285,7 +285,7 @@ test('adds a bam track with all the custom fields', async () => { '{"defaultRendering":"test"}', ]) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -295,7 +295,7 @@ test('adds a bam track from a url', async () => { await runCommand(['add-track', 'https://mysite.com/data/simple.bam']) - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -312,7 +312,7 @@ test('fails multiple assemblies exist but no assemblyNames passed', async () => 'copy', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -341,7 +341,7 @@ test('adds a plaintext gff', async () => { await runCommand(['add-track', simpleGff, '--load', 'copy']) expect(exists(ctxDir(ctx, 'volvox.sort.gff3'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -351,7 +351,7 @@ test('adds a plaintext vcf', async () => { await runCommand(['add-track', simpleVcf, '--load', 'copy']) expect(exists(ctxDir(ctx, 'volvox.filtered.vcf'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -360,7 +360,7 @@ test('adds a plaintext gtf', async () => { await initctx(ctx) await runCommand(['add-track', simpleGtf, '--load', 'copy']) expect(exists(ctxDir(ctx, 'volvox.sorted.gtf'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -371,7 +371,7 @@ test('adds a plaintext bed', async () => { expect(exists(ctxDir(ctx, 'volvox.bed'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -382,7 +382,7 @@ test('adds a plaintext bedpe', async () => { expect(exists(ctxDir(ctx, 'volvox.bedpe'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -395,7 +395,7 @@ test('adds a tabix gff with tbi', async () => { expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy() expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz.tbi'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -415,7 +415,7 @@ test('adds a tabix gff with csi', async () => { expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz'))).toBeTruthy() expect(exists(ctxDir(ctx, 'volvox.sort.gff3.gz.csi'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -433,7 +433,7 @@ test('adds a paf.gz file', async () => { ]) expect(exists(ctxDir(ctx, 'volvox_inv_indels.paf.gz'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -451,7 +451,7 @@ test('adds a paf file', async () => { ]) expect(exists(ctxDir(ctx, 'volvox_inv_indels.paf'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -468,7 +468,7 @@ test('adds a delta file', async () => { ]) expect(exists(ctxDir(ctx, 'volvox_inv_indels.delta'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -485,7 +485,7 @@ test('adds a mashmap file', async () => { ]) expect(exists(ctxDir(ctx, 'volvox_inv_indels.out'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -509,7 +509,7 @@ test('adds a mcscan simple anchors file', async () => { expect(exists(ctxDir(ctx, 'grape.bed'))).toBeTruthy() expect(exists(ctxDir(ctx, 'peach.bed'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -533,7 +533,7 @@ test('adds a mcscan anchors file', async () => { expect(exists(ctxDir(ctx, 'grape.bed'))).toBeTruthy() expect(exists(ctxDir(ctx, 'peach.bed'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) @@ -550,6 +550,6 @@ test('adds a chain file', async () => { 'copy', ]) expect(exists(ctxDir(ctx, 'volvox_inv_indels.chain'))).toBeTruthy() - expect(readConf(ctx)).toMatchSnapshot() + expect(readConf(ctx).tracks).toMatchSnapshot() }) }) diff --git a/products/jbrowse-cli/src/commands/admin-server-test-utils.ts b/products/jbrowse-cli/src/commands/admin-server-test-utils.ts deleted file mode 100644 index 068bde79b1..0000000000 --- a/products/jbrowse-cli/src/commands/admin-server-test-utils.ts +++ /dev/null @@ -1,29 +0,0 @@ -export function getPort(output: string) { - const portMatch = output.match(/localhost:([0-9]{4})/) - const port = portMatch?.[1] - if (!port) { - throw new Error(`Port not found in "${JSON.stringify(output)}"`) - } - return port -} - -export function getAdminKey(output: string) { - const keyMatch = output.match(/adminKey=([a-zA-Z0-9]{10,12}) /) - const key = keyMatch?.[1] - if (!key) { - throw new Error(`Admin key not found in "${output}"`) - } - return key -} - -export async function killExpress({ stdout }: { stdout: string }) { - // if (!stdout || typeof stdout !== 'string') { - // // This test didn't start a server - // return - // } - return fetch(`http://localhost:${getPort(stdout)}/shutdown`, { - method: 'POST', - headers: { 'Content-Type': 'application/json' }, - body: JSON.stringify({ adminKey: getAdminKey(stdout) }), - }) -} diff --git a/products/jbrowse-cli/src/commands/admin-server.test.ts b/products/jbrowse-cli/src/commands/admin-server.test.ts index 6674863fac..dd414a36b3 100644 --- a/products/jbrowse-cli/src/commands/admin-server.test.ts +++ b/products/jbrowse-cli/src/commands/admin-server.test.ts @@ -9,7 +9,6 @@ import { runCommand } from '@oclif/test' // locals import fetch from '../fetchWithProxy' import { dataDir, readConf, runInTmpDir } from '../testUtil' -import { getAdminKey, killExpress } from './admin-server-test-utils' const { copyFile, rename, chmod } = fs.promises @@ -22,6 +21,36 @@ const testIndex = dataDir('simpleIndex.html') // https://github.com/jestjs/jest/issues/14501 afterAll(() => (process.exitCode = 0)) +function getPort(output: string) { + const portMatch = output.match(/localhost:([0-9]{4})/) + const port = portMatch?.[1] + if (!port) { + throw new Error(`Port not found in "${JSON.stringify(output)}"`) + } + return port +} + +function getAdminKey(output: string) { + const keyMatch = output.match(/adminKey=([a-zA-Z0-9]{10,12}) /) + const key = keyMatch?.[1] + if (!key) { + throw new Error(`Admin key not found in "${output}"`) + } + return key +} + +async function killExpress({ stdout }: { stdout: string }) { + // if (!stdout || typeof stdout !== 'string') { + // // This test didn't start a server + // return + // } + return fetch(`http://localhost:${getPort(stdout)}/shutdown`, { + method: 'POST', + headers: { 'Content-Type': 'application/json' }, + body: JSON.stringify({ adminKey: getAdminKey(stdout) }), + }) +} + test('creates a default config', async () => { await runInTmpDir(async ctx => { await copyFile(testIndex, path.join(ctx.dir, path.basename(testIndex))) @@ -60,14 +89,14 @@ test('uses port 9090 if not specified', async () => { test('throws an error with a negative port', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['admin-server', '--port', '-10']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('throws an error with a port greater than 65535', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['admin-server', '--port', '66666']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) diff --git a/products/jbrowse-cli/src/commands/create.test.ts b/products/jbrowse-cli/src/commands/create.test.ts index 58cde0b6e7..3d5a6d3bd1 100644 --- a/products/jbrowse-cli/src/commands/create.test.ts +++ b/products/jbrowse-cli/src/commands/create.test.ts @@ -48,14 +48,14 @@ afterAll(() => (process.exitCode = 0)) test('fails if no path is provided to the command', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['create']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if no path is provided to the command, even with force', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['create', '--force']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -65,7 +65,7 @@ test('fails if user selects a directory that already has existing files', async .get('/jbrowse-web-v0.0.1.json') .reply(200, 'I am the wrong type', { 'Content-Type': 'application/json' }) const { error } = await runCommand(['create', '.']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if the fetch does not return the right file', async () => { @@ -76,7 +76,7 @@ test('fails if the fetch does not return the right file', async () => { '--url', 'https://example.com/jbrowse-web-v0.0.1.json', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -131,7 +131,7 @@ test('fails to download a version that does not exist', async () => { 'v999.999.999', '--force', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -141,7 +141,7 @@ test('fails because this directory is already set up', async () => { mockZip() await runCommand(['create', 'jbrowse']) const { error } = await runCommand(['create', 'jbrowse']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) diff --git a/products/jbrowse-cli/src/commands/set-default-session.test.ts b/products/jbrowse-cli/src/commands/set-default-session.test.ts index 4286c0231a..875cc0ba94 100644 --- a/products/jbrowse-cli/src/commands/set-default-session.test.ts +++ b/products/jbrowse-cli/src/commands/set-default-session.test.ts @@ -26,7 +26,7 @@ test('fails when no necessary default session information is provided', async () path.join(ctx.dir, 'config.json'), ) const { error } = await runCommand(['set-default-session']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -42,7 +42,7 @@ test('fails when default session is not readable', async () => { '--session', '{}', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails when file does not exist', async () => { @@ -57,7 +57,7 @@ test('fails when file does not exist', async () => { '--session', path.join(simpleDefaultSession, 'nonexist.json'), ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) @@ -74,7 +74,7 @@ test('fails when file is does not have a default session to read', async () => { '--session', simpleBam, ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('deletes a default session', async () => { diff --git a/products/jbrowse-cli/src/commands/text-index.test.ts b/products/jbrowse-cli/src/commands/text-index.test.ts index e3ff56706d..d766d10f86 100644 --- a/products/jbrowse-cli/src/commands/text-index.test.ts +++ b/products/jbrowse-cli/src/commands/text-index.test.ts @@ -57,14 +57,14 @@ afterAll(() => (process.exitCode = 0)) test('fails if no track ids are provided with --tracks flag.', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['text-index', '--tracks']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if there is an invalid flag', async () => { await runInTmpDir(async () => { const { error } = await runCommand(['text-index', '--Command']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) diff --git a/products/jbrowse-cli/src/commands/upgrade.test.ts b/products/jbrowse-cli/src/commands/upgrade.test.ts index 9798534d3c..0f4fe6711a 100644 --- a/products/jbrowse-cli/src/commands/upgrade.test.ts +++ b/products/jbrowse-cli/src/commands/upgrade.test.ts @@ -41,13 +41,13 @@ test('fails if user selects a directory that does not have a installation', asyn await runInTmpDir(async () => { mkdirSync('jbrowse') const { error } = await runCommand(['upgrade', 'jbrowse']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) }) test('fails if user selects a directory that does not exist', async () => { const { error } = await runCommand(['upgrade', 'jbrowse']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('upgrades a directory', async () => { @@ -114,7 +114,7 @@ test('fails to upgrade if version does not exist', async () => { .reply(404, {}) const { error } = await runCommand(['upgrade', '--tag', 'v999.999.999']) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() }) test('fails if the fetch does not return the right file', async () => { nock('https://example.com') @@ -125,5 +125,5 @@ test('fails if the fetch does not return the right file', async () => { '--url', 'https://example.com/JBrowse2-0.0.1.json', ]) - expect(error).toMatchSnapshot() + expect(error?.message).toMatchSnapshot() })