Merge pull request #97 from broadinstitute/gvda_ga4gh_tools_phase1

GA4GH Tool Execution Challenge Phase 1

scripts/ga4gh/tool_execution_challenge_phase1/README.txt

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+This document describes the protocol that was used to submit the entry "Cromwell via Google Genomics Pipelines API wdl_runner" in the GA4GH Tool Execution Challenge, Phase 1 (https://www.synapse.org/#!Synapse:syn8080305). 
+
+This protocol is based on the "Broad Institute GATK on Google Genomics" tutorial at https://cloud.google.com/genomics/v1alpha2/gatk, which demonstrates how to run a WDL pipeline through the Google Genomics Pipelines API wdl_runner.
+
+To replicate this work, change the GCS bucket paths and set the Google Project and local paths (which are set using environment variables in the protocol below) as appropriate.
+
+
+### Obtain challenge materials
+
+1. Get the raw WDL from https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/Dockstore.wdl and save to file ga4ghMd5.wdl
+
+2. Get the JSON content {"ga4ghMd5.inputFile": "md5sum.input"} and save to file ga4ghMd5.json
+
+3. Get the input text "this is the test file that will be used when calculating an md5sum" and save to file md5sum.input
+
+
+### Prepare for execution
+
+4. Add files to WDL repository under scripts/ga4gh/tool_execution_challenge_phase1 (need local copy of WDL and JSON to invoke in the execution command, plus a dummy workflow options file).
+
+5. Upload files to GCS at gs://ga4gh-tool-execution-challenge/phase1 (need copy of input file on GCS).
+
+
+### Execute through Google Genomics Pipelines API 
+
+6. Run the following command:
+
+````
+gcloud alpha genomics pipelines run \
+  --pipeline-file workflows/wdl_pipeline.yaml \
+  --zones us-central1-f \
+  --logging gs://ga4gh-tool-execution-challenge/phase1/logs \
+  --inputs-from-file WDL=${WDL_SCR}/ga4gh/tool_execution_challenge_phase1/ga4ghMd5.wdl \
+  --inputs-from-file WORKFLOW_INPUTS=${WDL_SCR}/ga4gh/tool_execution_challenge_phase1/ga4ghMd5.json \
+  --inputs-from-file WORKFLOW_OPTIONS=${WDL_SCR}/ga4gh/tool_execution_challenge_phase1/empty.options.json \
+  --inputs WORKSPACE=gs://ga4gh-tool-execution-challenge/phase1/work \
+  --inputs OUTPUTS=gs://ga4gh-tool-execution-challenge/phase1/out \
+  --project $P_OUTREACH
+````
+
+where ${WDL_SCR} is a local path to the WDL scripts directory.
+
+This returns `Running [operations/EOeigKSoKxi10d7o7tjQmHYg7qv-spECKg9wcm9kdWN0aW9uUXVldWU].`
+
+The status of the job can be monitored by running the following command: 
+
+````
+gcloud alpha genomics operations describe EOeigKSoKxi10d7o7tjQmHYg7qv-spECKg9wcm9kdWN0aW9uUXVldWU \
+    --format='yaml(done, error, metadata.events)'
+````
+
+When the job has completed successfully, this is what is returned:
+
+
+````
+done: true
+metadata:
+  events:
+  - description: start
+    startTime: '2017-02-28T11:35:14.458414638Z'
+  - description: pulling-image
+    startTime: '2017-02-28T11:35:14.458467173Z'
+  - description: localizing-files
+    startTime: '2017-02-28T11:35:56.281473416Z'
+  - description: running-docker
+    startTime: '2017-02-28T11:35:56.281499402Z'
+  - description: delocalizing-files
+    startTime: '2017-02-28T11:37:21.569738442Z'
+  - description: ok
+    startTime: '2017-02-28T11:37:23.273628610Z'
+````
+
+The output file md5sum.txt is written at gs://ga4gh-tool-execution-challenge/phase1/out and contains the result, 00579a00e3e7fa0674428ac7049423e2.
+
+
+

scripts/ga4gh/tool_execution_challenge_phase1/empty.options.json

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+{
+
+}

scripts/ga4gh/tool_execution_challenge_phase1/ga4ghMd5.json

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+{
+	"ga4ghMd5.inputFile": "gs://ga4gh-tool-execution-challenge/phase1/md5sum.input"
+}

scripts/ga4gh/tool_execution_challenge_phase1/ga4ghMd5.wdl

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+task md5 {
+  File inputFile
+
+  command {
+    /bin/my_md5sum ${inputFile}
+  }
+
+ output {
+    File value = "md5sum.txt"
+ }
+
+ runtime {
+   docker: "quay.io/briandoconnor/dockstore-tool-md5sum:1.0.2"
+   cpu: 1
+   memory: "512 MB"
+ }
+}
+
+workflow ga4ghMd5 {
+ File inputFile
+ call md5 { input: inputFile=inputFile }
+}

scripts/ga4gh/tool_execution_challenge_phase1/md5sum.input

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+this is the test file that will be used when calculating an md5sum

scripts/ga4gh/tool_execution_challenge_phase1/md5sum.txt

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+00579a00e3e7fa0674428ac7049423e2