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Jbrowse2 tool #3997

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Jbrowse2 tool #3997

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abretaud
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FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

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 server I had to hack a little as planemo doesn't support byte-range headers. I can probably share my notes if there's interest

@abretaud abretaud requested a review from hexylena September 30, 2021 15:40
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hexylena commented Oct 1, 2021

Love how much can be re-used for this, that's fantastic

@@ -350,14 +359,15 @@ cp $output.files_path/index.html $output;

<!-- TODO genetic code not yet supported in jbrowse2 https://github.com/GMOD/jbrowse-components/issues/1765 -->

<!-- TODO show linear view by default? -->
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+1

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Ah good we already support PAF files cannot wait for jb2! synteny, finally! :D

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Interesting, if you use config.json in the root, next to index.html, then it'll by default open on to a working jbrowse in the first assembly. Too easy.

image

bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request 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 this pull request Mar 30, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request 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 this pull request Mar 30, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request May 21, 2024
test data works
now to fix the tests too
bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request May 21, 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 this pull request May 21, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request May 21, 2024
test data works
now to fix the tests too
bgruening pushed a commit to bgruening/tools-iuc that referenced this pull request May 21, 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 this pull request May 21, 2024
rebasing to abreataud galaxyproject#3997 as requested by @hexylena
@bgruening bgruening mentioned this pull request May 21, 2024
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4 participants