Permalink
Browse files

Add documentation on running planemo against clusters.

  • Loading branch information...
jmchilton committed Apr 11, 2016
1 parent 7974e71 commit e0acf91bba6f0f6633e828e87cf78dc2a822817d
Showing with 50 additions and 4 deletions.
  1. +36 −4 docs/_writing_clusters.rst
  2. +14 −0 docs/writing/job_conf_slurm.xml
@@ -1,9 +1,9 @@
Cluster Usage
==============================

------------------------------
``GALAXY_SLOTS``
------------------------------
--------------------------------------------
Developing for Clusters - ``GALAXY_SLOTS``
--------------------------------------------

``GALAXY_SLOTS`` is a special environment variable that is set in a Galaxy
tool'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
a particular tool, check out `the Galaxy wiki
<https://wiki.galaxyproject.org/Admin/Config/GALAXY_SLOTS>`__.

.. _stringtie: https://ccb.jhu.edu/software/stringtie/
-----------------------------------------------
Test Against Clusters - ``--job_config_file``
-----------------------------------------------

The various commands that start Galaxy servers (``serve``,
``test``, ``shed_serve``, ``shed_test``, etc...) allow specification of
a Galaxy job configuration XML file (e.g. ``job_conf.xml``).

For instance, Slurm_ is a popular distributed reource manager (DRM) in the
Galaxy community. The following ``job_conf.xml`` tells Galaxy to run all jobs
using Slurm_ and allocate ``2`` cores for each job.

.. literalinclude:: writing/job_conf_slurm.xml
:language: xml

If this file is named ``planemo_job_conf.xml`` and resides in one's home
directory (``~``), Planemo can ``test`` or ``serve`` using this configuration
with the following commands.

::

planemo test --job_config_file ~/planemo_job_conf.xml .
planemo serve --job_config_file ~/planemo_job_conf.xml .

For general information on configuring Galaxy to communicate with clusters
check out `this page
<https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster>`__ on the
Galaxy wiki and for information regarding configuring job configuration XML
files in particular check out `the example
<https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced>`__
distributed with Galaxy.

.. _Slurm: http://slurm.schedmd.com/
@@ -0,0 +1,14 @@
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" />
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="drmaa">
<destination id="drmaa" runner="drmaa">
<param id="nativeSpecification">--time=00:05:00 --nodes=1 --ntasks=2</param>
</destination>
</destinations>
</job_conf>

0 comments on commit e0acf91

Please sign in to comment.