VCF-VCFintersect needs to be updated in the Main Tool Shed and Galaxy Test/Main servers

[jennaj]

Update tool shed then update test/main to correct usage issues (tool always errors).

Error

The Galaxy framework encountered the following error while attempting to run the tool:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/init.py", line 170, in prepare_job
job_wrapper.prepare()
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/init.py", line 897, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 445, in build
raise e
ValueError: invalid literal for int() with base 10: 'use_adv_controls'
Tool execution generated the following error message:
invalid literal for int() with base 10: 'use_adv_controls'

Github master: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfvcfintersect

Tool Shed repo: https://toolshed.g2.bx.psu.edu/repository?repository_id=fde54b460b1ce65c

Change from July that addresses the "use_adv_controls" code problem: 4cb83fa

Report at Biostars: https://biostar.usegalaxy.org/p/19440/

[martenson]

I pushed the whole updated Conda-only vcflib to the MTS

[martenson]

@natefoo do I need to do something special to update all of these on Main given it needs Conda to install its dependency?

[natefoo]

@martenson Can the suite be updated so I don't have to update each tool individually? Or would that not work for updates anyway?

[martenson]

@natefoo here you go, install this one: https://toolshed.g2.bx.psu.edu/view/devteam/suite_vcflib_1_0_0_rc1/2cafd05a4a59
https://toolshed.g2.bx.psu.edu/view/devteam/suite_vcflib_1_0_0_rc1/b506eeeb83c4

[martenson]

@natefoo do not install yet, there is no Conda package for one of the dependencies yet

[martenson]

@natefoo the suite should be fixed now and ready to install via Conda

https://toolshed.g2.bx.psu.edu/view/devteam/suite_vcflib_1_0_0_rc1/b506eeeb83c4

[natefoo]

Looks like they installed correctly, but the version string was bad for vcfsort:

galaxy.tools.toolbox.base DEBUG 2016-09-30 17:45:01,532 Loaded tool id: toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/@[email protected], version: @[email protected] into tool panel.

I have left the CVMFS transaction open so that if I should fix this manually I can do so, or just abort the transaction and start a new one once it's fixed.

[jennaj]

@martenson @natefoo ready to test or still undergoing changes?

[natefoo]

@jennaj No, the updates are not live in Main yet.

[martenson]

@natefoo that is an unexpanded macro token... no idea why that would happen. ping @bgruening @nsoranzo

[natefoo]

@martenson I found the problem - macros weren't included.

[martenson]

@natefoo well played!

[jennaj]

@natefoo @martenson Tested, still same error - maybe not in main yet?

[natefoo]

They were on Main, however they were not working due to a problem with the new conda-installed dependencies. This was fixed by switching to the use of --copy when creating conda environments for job runs and the fixing of a bug with --copy in galaxyproject/galaxy#3008.

VCF-VCF Intersect is working for me now. Hopefully the other vcflib tools work as well.

[jennaj]

This is still failing for me in my test history. Trying another.

[natefoo]

@jennaj If you're using rerun, select the new version of the tool. The old one won't work (and we should probably remove it).

[jennaj]

@natefoo Yes, passes with wrapper v 1.0.0_rc1.0 - thanks!

ps: Th older tool did not have that "a new tool version is available" banner on top of the re-run form. I think that threw me off. That missing is a problem, right? Captured it in this ticket: galaxyproject/galaxy#3021

[martenson]

splendid

[martenson]

@jennaj yeah, new ticket please

[jennaj]

Will do, thanks!

[jennaj]

Forgot to link ticket back. Testing it again, updates will go in there: galaxyproject/galaxy#3021