Jbrowse2 tool #3997
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Jbrowse2 tool #3997
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Love how much can be re-used for this, that's fantastic |
hexylena
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Feb 21, 2022
tools/jbrowse2/jbrowse2.xml
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| @@ -350,14 +359,15 @@ cp $output.files_path/index.html $output; | |||
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| <!-- TODO genetic code not yet supported in jbrowse2 https://github.com/GMOD/jbrowse-components/issues/1765 --> | |||
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| <!-- TODO show linear view by default? --> | |||
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Ah good we already support PAF files cannot wait for jb2! synteny, finally! :D |
…nd some track rendering options. Half broken/not finished
fubar2
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Jan 7, 2024
test data works now to fix the tests too
fubar2
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Jan 7, 2024
Amongst other things, this adds autoopening and adds track options back for JB2 - thanks! Fixed so passes biocontainers testing and various other odds and ends. Adds MAF (awaiting a bcbio PR) PAF and SPARQL not implemented yet. Uses json only - no calls to jbrowse command line tool
3 tasks
fubar2
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Jan 9, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
This was done via a command line diff of the two repositories, some test data has not been imported as part of this.
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Interesting, if you use
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(works from internet-less compute nodes + uses a properly frozen version)
bgruening
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Mar 30, 2024
test data works now to fix the tests too
bgruening
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Mar 30, 2024
Amongst other things, this adds autoopening and adds track options back for JB2 - thanks! Fixed so passes biocontainers testing and various other odds and ends. Adds MAF (awaiting a bcbio PR) PAF and SPARQL not implemented yet. Uses json only - no calls to jbrowse command line tool
bgruening
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Mar 30, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
bgruening
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Mar 30, 2024
test data works now to fix the tests too
bgruening
pushed a commit
to bgruening/tools-iuc
that referenced
this pull request
Mar 30, 2024
Amongst other things, this adds autoopening and adds track options back for JB2 - thanks! Fixed so passes biocontainers testing and various other odds and ends. Adds MAF (awaiting a bcbio PR) PAF and SPARQL not implemented yet. Uses json only - no calls to jbrowse command line tool
bgruening
pushed a commit
to bgruening/tools-iuc
that referenced
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Mar 30, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
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FOR CONTRIBUTOR:
This has been standing too long on my hard drive: here's a wrapper for jbrowse2 🎉 🎆 !
Implemented the same way as Jbrowse (though there might be other cool things to do now that it's more embeddable). I mostly copied the jbrowse1 wrapper, and tried to adapt.
It mostly works, but it needs some clean up, there are some options that are still there but don't work yet (or should be removed), some new datatypes to add support to, ....
An interesting thing in jbrowse2 is that many display options can be easily changed from the jbrowse ui (while in jbrowse1 it required tweaking json), which means I'm not sure if we need to (re)implement them all in the form...
Also to test with
planemo serverI had to hack a little as planemo doesn't support byte-range headers. I can probably share my notes if there's interest