Weekly lint and tests are failing

[lldelisle]

Hi, Here is a picture of the last weekly lint and tests:

Errored Tests

❌ ChIPseq_PE.ga_0

Execution Problem:

    [Errno 2] No such file or directory: '/tmp/tmp0m104th4/filtered BAM'

❌ gromacs-dctmd.ga_0

Execution Problem:

    Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy0 (version 2021.3+galaxy0)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmpcs5y89ad/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 337, in decorator\n    rval = func(self, trans, *args, **kwargs)\n  File \"/tmp/tmpcs5y89ad/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 830, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy0 (version 2021.3+galaxy0)\n"}

❌ gromacs-mmgbsa.ga_0

Execution Problem:

    Failed to find output [Complex topology] in invocation outputs [{}]

❌ pe-wgs-variation.ga_0

Execution Problem:

    Unexpected HTTP status code: 400: {"err_msg": "Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3 (version 2.0.3)", "err_code": 0, "traceback": "Traceback (most recent call last):\n  File \"/tmp/tmpfbprjxrq/galaxy-dev/lib/galaxy/web/framework/decorators.py\", line 337, in decorator\n    rval = func(self, trans, *args, **kwargs)\n  File \"/tmp/tmpfbprjxrq/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py\", line 830, in invoke\n    raise exceptions.MessageException(missing_tools_message)\ngalaxy.exceptions.MessageException: Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.3 (version 2.0.3)\n"}

❌ variation-reporting.ga_0

Execution Problem:

    Failed to find output [af_filter_threshold] in invocation outputs [{'all_variants_all_samples': {'id': 'a131cbc51f1fd9e9', 'src': 'hda', 'workflow_step_id': '4f6802b953fe5453'}, 'by_variant_report': {'id': '5a16b1422edd60d6', 'src': 'hda', 'workflow_step_id': 'b96161ff9e0be2b1'}, 'combined_variant_report': {'id': '030f0c55c98ae64e', 'src': 'hda', 'workflow_step_id': '8f470d64c61aa7d7'}, 'variant_frequency_plot': {'id': '270fb9fed54cf20c', 'src': 'hda', 'workflow_step_id': '6ced77daa85bcfc0'}}]

For more details, just download https://github.com/galaxyproject/iwc/suites/8800928810/artifacts/400205101

I checked the ChIPseq_PE which is failing. I rerun the CI on it (individually with a fake commit https://github.com/lldelisle/iwc/actions/runs/3281782971) and it passed...

[mvdbeek]

For your workflows we just need a new planemo release, I'm working on that. The 2 gromacs errors are real though .

[mvdbeek]

I think we've fixed those now, one of the VGP workflows fails because the outputs are slightly different, I'll get to that.