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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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Bamtools "Convert, Merge, Randomize BAM" was moved tools-devteam to tools-iuc but changes did not get pushed to MTS #2687

Open jennaj opened 4 years ago

jennaj commented 4 years ago

Full name: Convert, Merge, Randomize BAM datasets and perform other transformations (Galaxy Version 2.4.0)

Repo (last updated July 2017): https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools

MTS (last updated Jan 2017): https://toolshed.g2.bx.psu.edu/view/devteam/bamtools/04866f817daa

Test history (EU, but same results at ORG): https://usegalaxy.eu/u/jenj/h/test-bowtie2-mm10

Few PR items the update includes (a bit difficult to navigate):

  1. Usage re Collections: Right now merges all BAMs in the collection for each operation, no way to run tool per dataset in a collection. (was addressed in the update from what I can tell)
  2. Minor/Docs: the updated MTS dev repo link (definitely addressed)
  3. Functionality failure 1: "Convert to BED" fails with this error, always with collections, sometimes with individual datasets. (might be addressed -- the samtools or loc changes? forget the original issue and can't find PR but this was a known at one point -- dbkey wasn't linked up correctly).

terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check /data/dnb02/galaxy_db/job_working_directory/006/381/6381400/tool_script.sh: line 41: 4090180 Aborted bamtools convert -format bed -out /data/dnb02/galaxy_db/job_working_directory/006/381/6381400/galaxy_dataset_12936368.dat -in "localbam_0.bam" -in "localbam_1.bam"

  1. Functionality failure 2: "Random" fails with this in the GUI Unable to finish job but nothing in stderr/stdout.

The tool tests don't catch the functionality failures at usegalaxy.org, not sure about usegalaxy.eu. Maybe needs a few more tests?

https://jenkins.galaxyproject.org/view/tool_tests/job/tool%20tests%20against%20usegalaxy.org/lastCompletedBuild/testReport/toolshed.g2.bx.psu.edu_repos_devteam_bamtools_bamtools_2.4/

ping @davebx (already confirmed issue is actual)

bgruening commented 4 years ago

@martenson can you please check if IUC is admin in those repos?

jennaj commented 4 years ago

ping again .. MTS still not updated. This tool is in a tutorial, be nice if it worked. There isn't another way to get a bam > bed12 that I know of (?)

martenson commented 4 years ago

@bgruening bamtools, bamtools_filter, and bamtools_split are now administered by IUC, only the filter one was before; sorry I missed the ping

nsoranzo commented 4 years ago

I've manually updated the bamtools and bamtools_filter repositories on the MTS. For bamtools_split, it looks like it's a suite so I got these errors:

cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository [bamtools_split_paired] does not exist in the targeted Tool Shed.
Failed to update repository 'bamtools_split_paired' as it does not exist on the main Tool Shed.
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository bamtools_split updated successfully.
Repository metadata updated successfully for repository 'bamtools_split' on the main Tool Shed.
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository [bamtools_split_mapped] does not exist in the targeted Tool Shed.
Failed to update repository 'bamtools_split_mapped' as it does not exist on the main Tool Shed.
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository [bamtools_split_tag] does not exist in the targeted Tool Shed.
Failed to update repository 'bamtools_split_tag' as it does not exist on the main Tool Shed.
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository [bamtools_split_ref] does not exist in the targeted Tool Shed.
Failed to update repository 'bamtools_split_ref' as it does not exist on the main Tool Shed.
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git rev-parse HEAD
cd '/usr/users/ga002/soranzon/software/nsoranzo_tools-iuc/tool_collections/bamtools/bamtools_split' && git diff --quiet
Repository [suite_bamtools_2_4] does not exist in the targeted Tool Shed.
Failed to update repository 'suite_bamtools_2_4' as it does not exist on the main Tool Shed.
jennaj commented 4 years ago

MTS status:

Listed with devteam as the owner for all at MTS (original, expected)

Individual tools:

Just the old suite is there (expected from @nsoranzo 's comments): suite_bamtools_2_3_0

Repository bamtools revision c1a1bea37098 owned by devteam Repository bamtools_split revision 71dd32fb0b0a owned by devteam Repository package_bamtools_2_3_0_2d7685d2ae revision 7d6da4982f19 owned by devteam Repository bamtools_filter revision d64c7e752f4d owned by devteam

@martenson bamtools_split looks as if it still has the older "package" type of dependencies. So that needs to be updated then a new suite created (?). A bit confusing for me to sort out to explain what is actually wrong, so these are just guesses. But it would be nice to get these fixed up, in MTS, and installed on usegalaxy.* servers correctly :)