Lastz dependency issue at usegalaxy.org

[jennaj]

Error:

tool id: toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2 tool version: 1.2.2

job tool version:

job command line:

None

job stderr: python: can't open file '/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/lastz/0801f8207d30/lastz/lastz_wrapper.py': [Errno 2] No such file or directory /scratch/03166/xcgalaxy/main/staging/11624594/command.sh: line 40: /galaxy-repl/main/deps/samtools/0.1.18/env.sh: No such file or directory

[martenson]

I reinstalled the dependency and the package on Main, please re-test

[jennaj]

Thank you, in progress.

[jennaj]

Lastz works great now, thanks @martenson

[martenson]

thank you @jennaj

[jennaj]

The tool is problematic again: lastz_wrapper_2

Tool ID:

toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2

Error:

Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.

Could this be caused by the tool running out of memory? Should we bump it up?

ping @natefoo @martenson

[jennaj]

ping to check on the current status of the correction

[martenson]

lastz is not on the list of jobs killed by memory, so that is most probably not the issue

[natefoo]

Fixed in galaxyproject/usegalaxy-playbook@b51faf9bdb1333357ab654e47a995e2155f34acf.