Question: Galaxy is not loading job_conf.xml ?
0
gravatar for vebaev
2.8 years ago by
vebaev130
vebaev130 wrote:

Hi,

I have modified the job_conf.xml according the post of jmchilton so the tools can use multi-cores - https://biostar.usegalaxy.org/p/10158/#10261?

,nevertheless I noticed that bowtie2 still using 1 cpu core. 
So I spoiled the file inserting non xml test and Galaxy just load fine as before, which makes me think Galaxy is just lot loading the job_conf.xml on the first place (my thoughts)?

I have the file in the same place as galaxy.ini

-rw-r--r--. 1 1450 1450 49120 Aug  4 14:29 galaxy.ini
-rwxr-xr-x. 1 1450 1450  1115 Aug  4 14:35 job_conf.xml

 

and the content is:

<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
        <plugin id="multilocal" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
    </plugins>
    <handlers>
       <handler id="main" />
    </handlers>

  <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="multicore8" runner="multilocal">
          <param id="local_slots">8</param>
       </destination>
  </destinations>

    <tools>
      <tool id="bowtie2" destination="multicore8" />
      <tool id="bowtie"  destination="multicore8" />
      <tool id="deeptools"  destination="multicore8" />
      <tool id="cufflinks" destination="multicore8" />
      <tool id="cuffdiff"  destination="multicore8" />
      <tool id="cuffmerge" destination="multicore8" />
      <tool id="tophat2" destination="multicore8" />
    </tools>
</job_conf>

 

 

job config • 957 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by vebaev130
3
gravatar for Hotz, Hans-Rudolf
2.8 years ago by
Switzerland
Hotz, Hans-Rudolf1.7k wrote:

just double checking: what is the setting of 'job_config_file' in galaxy.ini ?

Hans-Rudolf

 

 

 

ADD COMMENTlink written 2.8 years ago by Hotz, Hans-Rudolf1.7k

Thanks a lot! :) I totally forgot about that option which was # in the galaxy.ini, I just was modifying the job_conf file like hell :)

ADD REPLYlink written 2.8 years ago by vebaev130
1
gravatar for vebaev
2.8 years ago by
vebaev130
vebaev130 wrote:

Issue is solved - look the comment from Hans-Rudolf above :)

ADD COMMENTlink written 2.8 years ago by vebaev130

Hello, If you have time, please accept Hans-Rudolf's answer so that others will find the solution should they run into the same situation. (I moved the comment to a reply so that it is now accessible). Thanks, Jen, Galaxy team

ADD REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k

done :)           

ADD REPLYlink written 2.8 years ago by vebaev130
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