11Cluster Usage
22==============================
33
4- ------------------------------
5- ``GALAXY_SLOTS ``
6- ------------------------------
4+ --------------------------------------------
5+ Developing for Clusters - ``GALAXY_SLOTS ``
6+ --------------------------------------------
77
88``GALAXY_SLOTS `` is a special environment variable that is set in a Galaxy
99tool's runtime environment. If the tool you are working on allows configuring
@@ -28,4 +28,36 @@ For information on how server administrators can configure this value for
2828a particular tool, check out `the Galaxy wiki
2929<https://wiki.galaxyproject.org/Admin/Config/GALAXY_SLOTS> `__.
3030
31- .. _stringtie : https://ccb.jhu.edu/software/stringtie/
31+ -----------------------------------------------
32+ Test Against Clusters - ``--job_config_file ``
33+ -----------------------------------------------
34+
35+ The various commands that start Galaxy servers (``serve ``,
36+ ``test ``, ``shed_serve ``, ``shed_test ``, etc...) allow specification of
37+ a Galaxy job configuration XML file (e.g. ``job_conf.xml ``).
38+
39+ For instance, Slurm _ is a popular distributed reource manager (DRM) in the
40+ Galaxy community. The following ``job_conf.xml `` tells Galaxy to run all jobs
41+ using Slurm _ and allocate ``2 `` cores for each job.
42+
43+ .. literalinclude :: writing/job_conf_slurm.xml
44+ :language: xml
45+
46+ If this file is named ``planemo_job_conf.xml `` and resides in one's home
47+ directory (``~ ``), Planemo can ``test `` or ``serve `` using this configuration
48+ with the following commands.
49+
50+ ::
51+
52+ planemo test --job_config_file ~/planemo_job_conf.xml .
53+ planemo serve --job_config_file ~/planemo_job_conf.xml .
54+
55+ For general information on configuring Galaxy to communicate with clusters
56+ check out `this page
57+ <https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster> `__ on the
58+ Galaxy wiki and for information regarding configuring job configuration XML
59+ files in particular check out `the example
60+ <https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced> `__
61+ distributed with Galaxy.
62+
63+ .. _Slurm : http://slurm.schedmd.com/
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