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Recommended settings for shared filesystem setup #209

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scholtalbers opened this issue Nov 12, 2019 · 0 comments
Open

Recommended settings for shared filesystem setup #209

scholtalbers opened this issue Nov 12, 2019 · 0 comments

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@scholtalbers
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I have some difficulties setting up, what I think is a basic pulsar setup. I want to run a specific local tool with e.g. python $__tool_directory__/tool.py on a remote system. The remote system has the same shared filesystem as the galaxy server and I can run pulsar with the same user. I tried with default_file_action=none but then the tool.py is not found. With remote_copy that part works, but the input files gets unnecessarily staged.. In addition, with this setting I get the following error:

Traceback (most recent call last):
  File "/tmpdata/pulsar/files/staging/145701/tool_files/dataset_export.py", line 32, in <module>
    with open(script_path / "config.yaml") as c:
FileNotFoundError: [Errno 2] No such file or directory: '/tmpdata/pulsar/files/staging/145701/tool_files/config.yaml

This is set in the pulsar app.yml:

conda_auto_init: true
conda_auto_install: true
staging_directory: /tmpdata/pulsar/files/staging
persistence_directory: /tmpdata/pulsar/files/persisted_data
tool_dependency_dir: /tmpdata/pulsar/dependencies

This in galaxy's job_conf.xml

<plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner">
</plugin>
<destination id="pulsar_remote" runner="pulsar_rest">
          <param id="url">http://remote:8913/</param>
          <param id="private_token">xxx</param>
          <param id="default_file_action">remote_copy</param>
</destination>

What would be the right settings for my setup?

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