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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
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 withdefault_file_action=none
but then thetool.py
is not found. Withremote_copy
that part works, but the input files gets unnecessarily staged.. In addition, with this setting I get the following error:This is set in the pulsar app.yml:
This in galaxy's
job_conf.xml
What would be the right settings for my setup?
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