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job_conf.xml.sample_advanced
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job_conf.xml.sample_advanced
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<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<!-- "workers" is the number of threads for the runner's work queue.
The default from <plugins> is used if not defined for a <plugin>.
-->
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
<plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner" workers="2"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Different DRMs handle successfully completed jobs differently,
these options can be changed to handle such differences and
are explained in detail on the Galaxy wiki. Defaults are shown -->
<param id="invalidjobexception_state">ok</param>
<param id="invalidjobexception_retries">0</param>
<param id="internalexception_state">ok</param>
<param id="internalexception_retries">0</param>
</plugin>
<plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
<param id="drmaa_library_path">/sge/lib/libdrmaa.so</param>
</plugin>
<plugin id="lwr" type="runner" load="galaxy.jobs.runners.lwr:LwrJobRunner">
<!-- More information on LWR can be found at https://lwr.readthedocs.org -->
<!-- Uncomment following line to use libcurl to perform HTTP calls (defaults to urllib) -->
<!-- <param id="transport">curl</param> -->
</plugin>
<plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" />
<plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" />
<plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" />
</plugins>
<handlers default="handlers">
<!-- Additional job handlers - the id should match the name of a
[server:<id>] in universe_wsgi.ini.
-->
<handler id="handler0" tags="handlers"/>
<handler id="handler1" tags="handlers"/>
<!-- Handlers will load all plugins defined in the <plugins> collection
above by default, but can be limited to a subset using <plugin>
tags. This is useful for heterogenous environments where the DRMAA
plugin would need to be loaded more than once with different
configs.
-->
<handler id="sge_handler">
<plugin id="sge"/>
</handler>
<handler id="special_handler0" tags="special_handlers"/>
<handler id="special_handler1" tags="special_handlers"/>
<handler id="trackster_handler"/>
</handlers>
<destinations default="local">
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources.
-->
<destination id="local" runner="local"/>
<destination id="pbs" runner="pbs" tags="mycluster"/>
<destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs">
<!-- Define parameters that are native to the job runner plugin. -->
<param id="Resource_List">walltime=72:00:00</param>
</destination>
<destination id="remote_cluster" runner="drmaa" tags="longjobs"/>
<destination id="real_user_cluster" runner="drmaa">
<!-- TODO: The real user options should maybe not be considered runner params. -->
<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="dynamic" runner="dynamic">
<!-- A destination that represents a method in the dynamic runner. -->
<param id="function">foo</param>
</destination>
<destination id="secure_lwr" runner="lwr">
<param id="url">https://windowshost.examle.com:8913/</param>
<!-- If set, private_token must match token remote LWR server configured with. -->
<param id="private_token">123456789changeme</param>
<!-- Uncomment the following statement to disable file staging (e.g.
if there is a shared file system between Galaxy and the LWR
server). Alternatively action can be set to 'copy' - to replace
http transfers with file system copies. -->
<!-- <param id="default_file_action">none</param> -->
<!-- The above option is just the default, the transfer behavior
none|copy|http can be configured on a per path basis via the
following file. See lib/galaxy/jobs/runners/lwr_client/action_mapper.py
for examples of how to configure this file. This is very beta
and nature of file will likely change.
-->
<!-- <param id="file_action_config">file_actions.json</param> -->
<!-- Uncomment following option to disable Galaxy tool dependency
resolution and utilize remote LWR's configuraiton of tool
dependency resolution instead (same options as Galaxy for
dependency resolution are available in LWR).
-->
<!-- <param id="dependency_resolution">remote</params> -->
<!-- Uncomment following option to enable setting metadata on remote
LWR server. The 'use_remote_datatypes' option is available for
determining whether to use remotely configured datatypes or local
ones (both alternatives are a little brittle). -->
<!-- <param id="remote_metadata">true</param> -->
<!-- <param id="use_remote_datatypes">false</param> -->
<!-- If remote LWR server is configured to run jobs as the real user,
uncomment the following line to pass the current Galaxy user
along. -->
<!-- <param id="submit_user">$__user_name__</param> -->
<!-- Various other submission parameters can be passed along to the LWR
whose use will depend on the remote LWR's configured job manager.
For instance:
-->
<!-- <param id="submit_native_specification">-P bignodes -R y -pe threads 8</param> -->
</destination>
<destination id="ssh_torque" runner="cli">
<param id="shell_plugin">SecureShell</param>
<param id="job_plugin">Torque</param>
<param id="shell_username">foo</param>
<param id="shell_hostname">foo.example.org</param>
<param id="job_Resource_List">walltime=24:00:00,ncpus=4</param>
</destination>
<destination id="condor" runner="condor">
<!-- With no params, jobs are submitted to the 'vanilla' universe with:
notification = NEVER
getenv = true
Additional/override query ClassAd params can be specified with
<param> tags.
-->
<param id="request_cpus">8</param>
</destination>
</destinations>
<tools>
<!-- Tools can be configured to use specific destinations or handlers,
identified by either the "id" or "tags" attribute. If assigned to
a tag, a handler or destination that matches that tag will be
chosen at random.
-->
<tool id="foo" handler="trackster_handler">
<param id="source">trackster</param>
</tool>
<tool id="bar" destination="dynamic"/>
<tool id="baz" handler="special_handlers" destination="bigmem"/>
</tools>
<limits>
<!-- Certain limits can be defined. -->
<limit type="registered_user_concurrent_jobs">2</limit>
<limit type="unregistered_user_concurrent_jobs">1</limit>
<limit type="job_walltime">24:00:00</limit>
<limit type="concurrent_jobs" id="local">1</limit>
<limit type="concurrent_jobs" tag="mycluster">2</limit>
<limit type="concurrent_jobs" tag="longjobs">1</limit>
</limits>
</job_conf>