Question: (Closed) Galaxy tool multi-threading
0
TWV • 20 wrote:
I have a local instance of galaxy running on a PC with 4 cores (8 threads). When I run a blast, bowtie2 or other similar job, they only ever use 1 thread.
I have read that it is possible to setup which tools should use how many jobs by editing config/job_conf.xml. I adapted the setup made in https://biostar.usegalaxy.org/p/10158/ to be used on my PC:
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
<plugin id="multilocal" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
</plugins>
<handlers>
<handler id="main" />
</handlers>
<destinations default="local">
<destination id="local" runner="local"/>
<destination id="multicore4" runner="multilocal">
<param id="local_slots">4</param>
</destination>
</destinations>
<tools>
<tool id="bowtie2" destination="multicore4" />
<tool id="bowtie" destination="multicore4" />
<tool id="deeptools" destination="multicore4" />
<tool id="cufflinks" destination="multicore4" />
<tool id="cuffdiff" destination="multicore4" />
<tool id="cuffmerge" destination="multicore4" />
<tool id="tophat2" destination="multicore4" />
</tools>
</job_conf>
If I am no mistaken, this way 4 cores will be reserved for 4 single-threaded jobs, and the other 4 are reserved for the listed tools which will be run one job at a time with 4 cores, am I right? Did I miss or misunderstand something?
Also related: https://biostar.usegalaxy.org/p/23270
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