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Merge pull request #5881 from moskalenko/doc

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Update cluster docs for virtualenv issue in drmaa real user jobs
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Martin Cech
2018-04-12 14:24:04 -04:00
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parent 1583db76eb 2cec29c043
commit 1bc1720ea8
1 changed files with 6 additions and 1 deletions
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doc/source/admin/cluster.md
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@@ -348,7 +348,12 @@ galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/external_chown_script
If your sudo config contains `Defaults requiretty`, this option must be disabled.
For Galaxy releases > 17.05, the sudo call has been moved to `galaxy.yml` and is thereby configurable by the Galaxy admin. This can be of interest because sudo removes `PATH`, `LD_LIBRARY_PATH`, etc. variables per default in some installations. In such cases the sudo calls in the three variables in galaxy.yml can be adapted, e.g., `sudo -E PATH=... LD_LIBRARY_PATH=... /PATH/TO/GALAXY/scripts/drmaa_external_runner.py`. In order to allow setting the variables this way adaptions to the sudo configuration might be necessary.
For Galaxy releases > 17.05, the sudo call has been moved to `galaxy.yml` and is thereby configurable by the Galaxy admin. This can be of interest because sudo removes `PATH`, `LD_LIBRARY_PATH`, etc. variables per default in some installations. In such cases the sudo calls in the three variables in galaxy.yml can be adapted, e.g., `sudo -E PATH=... LD_LIBRARY_PATH=... /PATH/TO/GALAXY/scripts/drmaa_external_runner.py`. In order to allow setting the variables this way adaptions to the sudo configuration might be necessary. For example, the path to the python inside the galaxy's python virtualenv may have to be inserted before the script call to make sure the virtualenv is used for drmaa submissions of real user jobs.
```
drmaa_external_runjob_script: sudo -E .venv/bin/python scripts/drmaa_external_runner.py --assign_all_groups
```
Also for Galaxy releases > 17.05: In order to allow `external_chown_script.py` to chown only path below certain entry points the variable `ALLOWED_PATHS` in the python script can be adapted. It is sufficient to include the directorries `job_working_directory` and `new_file_path` as configured in `galaxy.yml`.
It is also a good idea to make sure that only trusted users, e.g. root, have write access to all three scripts.