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added documentation for GALAXY_MEMORY_MB #801

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jmchilton merged 1 commit into from
Mar 13, 2018
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added documentation for GALAXY_MEMORY_MB #801

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14 changes: 11 additions & 3 deletions docs/_writing_clusters.rst
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
Cluster Usage
==============================

--------------------------------------------
Developing for Clusters - ``GALAXY_SLOTS``
--------------------------------------------
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Developing for Clusters - ``GALAXY_SLOTS``, ``GALAXY_MEMORY_MB``, and ``GALAXY_MEMORY_MB_PER_SLOT``
-----------------------------------------------------------------------------------------------------

``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
Expand All @@ -30,6 +30,14 @@ 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>`__.

Analogously ``GALAXY_MEMORY_MB`` and ``GALAXY_MEMORY_MB_PER_SLOT`` are special
environment variables in a Galaxy tool's runtime environment that can be used
to specify the amount of memory that a tool can use overall and per slot,
respectively.

For an example see the samtools sort tool (`here https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/samtools/samtools_sort/samtools_sort.xml`__) which allows to specify the
total memory with the -m parameter.

-----------------------------------------------
Test Against Clusters - ``--job_config_file``
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