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Small doc fixes

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This commit is contained in:
Nicola Soranzo
2018-03-13 16:51:17 +00:00
committed by GitHub
parent 4a59f30209
commit b92a5e1b47
1 changed files with 6 additions and 7 deletions
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doc/source/admin/cluster.md
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@@ -355,9 +355,9 @@ It is also a good idea to make sure that only trusted users, e.g. root, have wri
Some maintenance and support of this code will be provided via the usual [Support](https://galaxyproject.org/support/) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team.
## Special environment variables for parallel jobs
## Special environment variables for job resources
Galaxy *tries* to define special enironment variables for each job that contain
Galaxy *tries* to define special environment variables for each job that contain
the information on the number of available slots and the amount of available
memory:
@@ -371,14 +371,13 @@ tries to determine these values. This bash code is defined here:
* lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
* lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
If this code is unable to determine the variables then they will not be set.
Therefore in the tool xml files the variables should be used with a default,
e.g. `\${GALAXY_SLOTS:-DEFAULT}` (see also https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage).
If this code is unable to determine the variables, then they will not be set.
Therefore in the tool XML files the variables should be used with a default,
e.g. `\${GALAXY_SLOTS:-1}` (see also https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage).
In particular `GALAXY_MEMORY_MB` and `GALAXY_MEMORY_MB_PER_SLOT` are currently
defined only for a few cluster types. Contributions are very welcome, e.g. let
the Galaxy development mailing list know how to modify that file to support
it.
the Galaxy developers know how to modify that file to support your cluster.
## Contributors