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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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Is pulsar-check expected to work currently? #377

Open hexylena opened 1 week ago

hexylena commented 1 week ago 
INFO:pulsar.client.manager:Setting Pulsar client class to standard, non-caching variant.
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/t/script.py] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/dataset_0.dat] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/dataset_0_files/input_subdir/extra] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/metadata/12312231231231.dat] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/w/config.txt] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/m/metadata_test123] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/seq/human_full_seqs] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/bwa/human.fa.fai] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/bwa/human.fa] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/w/config.txt] (action_type: [message])
Traceback (most recent call last):
  File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 318, in run
    assert result_status["returncode"] == 4, f"Expected exit code of 4, got {result_status['returncode']} - {std_streams_debug}"
AssertionError: Expected exit code of 4, got 127 - actual stdout [], actual stderr [/mnt/pulsar/files/staging/123456/command.sh: line 112: python: command not found
]
Traceback (most recent call last):
  File "/mnt/pulsar/venv/bin/pulsar-check", line 8, in <module>
    sys.exit(main())
  File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 607, in main
    run(options)
  File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 318, in run
    assert result_status["returncode"] == 4, f"Expected exit code of 4, got {result_status['returncode']} - {std_streams_debug}"
AssertionError: Expected exit code of 4, got 127 - actual stdout [], actual stderr [/mnt/pulsar/files/staging/123456/command.sh: line 112: python: command not found
]

I keep seeing this and figured i'd report it in case it's useful. python3 would've worked, or if the venv was included on path since that includes a python