# NCBI+ blastp and GALAXY\_SLOTS - increase number of threads

**URL:** <https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326>\
**Category:** Uncategorized\
**Tags:** devops-administration, ncbi, galaxy-local, blast, blastp\
**Created:** [December 15, 2023, 7:33pm UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326 "2023-12-15T19:33:01Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![prao123](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/prao123/32/2456_2.png) [@prao123](https://help.galaxyproject.org/u/prao123)\
**Post date:** [December 15, 2023, 7:33pm UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326/1 "2023-12-15T19:33:01Z")

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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:

```auto
<?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!

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [December 15, 2023, 11:58pm UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326/2 "2023-12-15T23:58:37Z")

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Hi @prao123

I cross-posted your question over to the Admin chat. They may reply here or there, and feel free to join the chat. [You're invited to talk on Matrix](https://matrix.to/#/!rfLDbcWEWZapZrujix:gitter.im/$6J37j76Ttz2Z_l-ZzHrJeewrf7SpL4FG-Vq_OeRhOZU?via=gitter.im&via=matrix.org)

Meanwhile, the tutorials may also help, along with this recent Q&A.

> [@Increasing cores](https://help.galaxyproject.org/t/increasing-cores/11267/6):
>
> Hi, you can find the resources here: [tpv-shared-database/tools.yml at main · galaxyproject/tpv-shared-database · GitHub](https://github.com/galaxyproject/tpv-shared-database/blob/main/tools.yml#L2421) which is shared across Galaxy instances and then local overwrites for EU here: [infrastructure-playbook/files/galaxy/tpv/tools.yml at master · usegalaxy-eu/infrastructure-playbook · GitHub](https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/tpv/tools.yml) ${GALAXY\_SLOTS:-1} is a bash syntax and just states that if the environment variable GALAXY\_SLOTS is not set, then default to 1 core. We do set GALAXY\_SLOTS with the values given in the linked resources files. What is your scientific question you want to answer? There might be a better way to solve your problem that does not involve mafft. Ciao, Bjoern

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**Author:** ![bernt-matthias](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bernt-matthias/32/502_2.png) [@bernt-matthias](https://help.galaxyproject.org/u/bernt-matthias)\
**Post date:** [December 16, 2023, 11:01am UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326/3 "2023-12-16T11:01:56Z")

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My first guess would be that the used tool id is wrong. For blastp the id is `ncbi_blastp_wrapper`, [see here](https://github.com/peterjc/galaxy_blast/blob/2dd12dc4b078ed9f8c2cbfc1cfc19a361812753b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml#L1C11-L1C30).

Note that for small instances the `job_conf.xml` is sufficient for configuring ressources. The TPV method cited by @jennaj seems to be better on the long run (maybe even for smaller instances).

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**Author:** ![prao123](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/prao123/32/2456_2.png) [@prao123](https://help.galaxyproject.org/u/prao123)\
**Post date:** [December 19, 2023, 5:54pm UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326/4 "2023-12-19T17:54:34Z")

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Sometimes the most inane thing that I forget is the solution! I changed the tool id to “ncbi\_blastp\_wrapper” and it worked!

Thank you for that solution!

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<div class="post-metadata">

**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [March 17, 2026, 4:43am UTC](https://help.galaxyproject.org/t/ncbi-blastp-and-galaxy-slots-increase-number-of-threads/11326/5 "2026-03-17T04:43:53Z")

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