Hello Galaxy team!
We are running a local Galaxy installation which is set on a server with multiple cores. I executed a job for searching peptides against the NCBI-nr database querying 5000 peptides against the NCBI-nr database. The query is taking quite long. For speeding up the process, we edited a tool_conf.xml template to tell Galaxy to use more threads using the “local_slots” parameter set to 16.
We tested the this conf file using TopHat and it works as expected i.e. TopHat takes the num_threads parameter from the job_conf.xml file. However, when using BLAST+ blastp (v2.14 or v2.10), the operation resorts back to 1 thread. Our job_conf.xml file is as follows:
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is
configured by default (if there is no explicit config). -->
<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"/>
<plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="1"/>
</plugins>
<!--
<handlers>
<handler id="main" />
</handlers>
-->
<destinations default="local">
<destination id="local" runner="local"/>
<destination id="multicore16" runner="multilocal">
<param id="local_slots">16</param>
</destination>
<destination id="mccli16" runner="cli">
<param id="local_slots">16</param>
</destination>
</destinations>
<tools>
<tool id="bowtie2" destination="multicore16" />
<tool id="bowtie" destination="multicore16" />
<tool id="tophat2" destination="multicore16" />>
<tool id="blast" destination="mccli16" />
<tool id="blastp" destination="mccli16" />
<tool id="ncbi_blast_plus" destination="mccli16" />
</tools>
</job_conf>
Navigating down the rabbit hole of connected files, we are still not able to figure out why TopHat takes the parameters from job_conf.xml but ncbi-blastp+ does not. We assume that blastp is taking the number_threads parameter from some other file.
My question is: Which file specifies the parameter for increasing the number of threads for the blastp tool? Or
How can we increase the number of threads for the blastp tool?
Thank you!