Question: tools, uploading, clusters and destinations
0
gravatar for colindaven
10 months ago by
colindaven0
colindaven0 wrote:

Hi,

we have a local Galaxy 17.05 linked up to a SLURM cluster. Since upload and some downloads (eg. tools upload1 and ucsc_table_direct1) were not working, we configured the job_config.xml as follows so these jobs only run on the local machine, not on the cluster

    <tools>
<tool id="upload1" destination="local_no_container" />
<tool id="ucsc_table_direct1" destination="local_no_container" />
<tool id="ebi_sra_main" destination="local_no_container" />
<tool id="microbial_import1" destination="local_no_container" />
<tool id="biomart" destination="local_no_container" />
<tool id="modmine" destination="local_no_container" />
<tool id="mousemine" destination="local_no_container" />
<tool id="ratmine" destination="local_no_container" />
<tool id="metabolicmine" destination="local_no_container" />
<tool id="zebrafishmine" destination="local_no_container" />
<tool id="eupathdb" destination="local_no_container" />
<tool id="hbvar" destination="local_no_container" />
<tool id="genomespace_file_browser_prod" destination="local_no_container" />
</tools>

However, now ALL jobs (not just the listed ones) are running on the local machine. The default queue is still "slurm8threads - see below" which had been working flawlessly up till the the above tool id changes.

Is there a way to set all other tools apart from those listed to run on the default destination, slurm8threads, or do we have to list ALL tools ?

Thanks.

  <destinations default_from_environ="GALAXY_DESTINATIONS_DEFAULT" default="slurm8threads">

galaxy@hpc-vm3:/home/rcug$ env | grep GAL GALAXY_DESTINATIONS_DEFAULT=slurm8threads

    <destination id="slurm8threads" runner="slurm">
    <env file="/lager2/rcug/RCUT/galaxy/galaxy/.venv/bin/activate"/>
    <env id="_JAVA_OPTIONS">-Xmx6g -Dhttp.proxyHost=172.24.2.50 -Dhttp.proxyPort=8080 -Dhttps.proxyHost=172.24.2.50 -Dhttps.proxyPort=8080</env>
    <param id="request_cpus">8</param>
    <param id="embed_metadata_in_job">False</param>
    <param id="nativeSpecification">-p galaxy -n 8</param>
</destination>
admin • 269 views
ADD COMMENTlink modified 10 months ago by Hotz, Hans-Rudolf1.8k • written 10 months ago by colindaven0
1
gravatar for Hotz, Hans-Rudolf
10 months ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi

Just by comparing with our job_config.xml file, I suggest:

    <destinations default="slurm8threadsl">
      <destination id="local" runner="local" />
      <destination id="slurm8threads" runner="slurm"   ...etc. />
    </destinations>

Regards, Hans-Rudolf

ADD COMMENTlink written 10 months ago by Hotz, Hans-Rudolf1.8k

Thanks, I had been having problems with the default_from_environ="GALAXY_DESTINATIONS_DEFAULT"

already. I deleted this and solved the problem.

ADD REPLYlink written 10 months ago by colindaven0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 154 users visited in the last hour