Re: galaxy-dev Digest, Vol 134, Issue 19

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Re: galaxy-dev Digest, Vol 134, Issue 19

Matthias Bernt
Dear ...,

what are the file permissions for the file and the folder?

Is the drmaa_external_runner.py python script run with sudo?

Which release/branch are you on?

Best,
Matthias




> We are setting up run as real user but have run into a strange issue.
> When the drmaa external script is called it could not load the job json
> file. All permissions are set properly and the file exists. Upon
> attempting to run the script by itself this error is created. When
> loading a test script to open a file there is no issue. If the drmaa
> external script is run as root the same issue occurs.
>
> /mnt/ceph/home/galaxy/galaxy/files_directory/database/slurm/11.jt_json
> Traceback (most recent call last):
>     File "scripts/drmaa_external_runner.py", line 157, in <module>
>       main()
>     File "scripts/drmaa_external_runner.py", line 146, in main
>       load_job_template_from_file(jt, json_filename)
>     File "scripts/drmaa_external_runner.py", line 43, in
> load_job_template_from_file
>       f = open(filename, 'r')
> IOError: [Errno 13] Permission denied:
> '/mnt/ceph/home/galaxy/galaxy/files_directory/database/slurm/11.jt_json'

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