Question: galaxy local installation
gravatar for janecao999
7 months ago by
janecao9990 wrote:


I recently installed a local instance of galaxy (v18.0) on a linux server and configured galaxy to work with apache and proftpd. The galaxy worked well when there is no job_conf.xml given under config/ directory. The galaxy could start without errors when job_conf.xml is used (job_conf.xml is just a copy of job_conf.xml.sample_basic) , but all jobs submitted stayed as gray and can't be pushed to "running" status. The galaxy documentation states that galaxy runs with the configuration as defined in job_conf.xml.sample_basic when no job_conf.xml is given in config/ directory, so I assumed that galaxy should work with or without job_conf.xml. Did I miss something?

In the old version of galaxy, we can define tool_runners in universe_wsgi.ini file. The jobs run in local can be defined such as "cat1 = local:///" and the jobs run in cluster can be defined such as "tophat = drmaa://-pe galaxy 4". Can I copy the tool_runners defined in universed_wsgi.ini to galaxy.yml file used in the new version of galaxy? If it is necessary to configure them in job_conf.xml, is there an example file I can use as reference (for example, cat1 run locally and tophat run in computing node/cluster)?

Thank a lot for your help!


galaxy • 451 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by janecao9990
gravatar for Martin Čech
7 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

You might be affected by the bug in this PR so please make sure you don't have <handlers> specified (unless you need to) in the job_conf.xml.

The universe_wsgi.ini is quite old name for Galaxy's configfile therefore I suggest not copying any settings and looking into the documentation on job configuration for 18.01 instead:

ADD COMMENTlink modified 7 months ago • written 7 months ago by Martin Čech ♦♦ 4.9k

Issue solved after comment out <handlers> lines.
Thanks a lot, Martin!

ADD REPLYlink written 7 months ago by janecao9990

I created job_conf.xml file and make local as default and a few alignment programs to run in cluster (sge_default). The jobs submitted to default/local worked well, but jobs to sge_default cannot be pushed to queuing system. The job_conf.xml is:

<?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). -->
        <plugin id="local" type="runner" load="" workers="4"/>
        <plugin id="drmaa_default" type="runner" load="" />
    <destinations default="local">
        <destination id="local" runner="local">
            <param id="local_slots">2
        <destination id="sge_default" runner="drmaa_default">
            <param id="nativeSpecification">-pe shared 4 -l highp -l h_rt=24:00:00
       <tool id="tophat" destination="sge_default" />
       <tool id="bowtie2" destination="sge_default" />
       <tool id="bowtie_wrapper" destination="sge_default" />
       <tool id="bwa_wrapper" destination="sge_default" />

For example, after tophat was submitted, a job script can be found in database/jobs_directory. But, I cannot see it in sge queuing system (qstat). There is no script found in database/pbs directory as in the old system.

Where should I look at to solve the issue or any misconfiguration in job_conf.xml file?

Thank you for your help!


edit by moderator: use triple-tick quotation for indented code

ADD REPLYlink written 7 months ago by janecao9990

I suggest you create a new question to improve visibility.

ADD REPLYlink written 7 months ago by Martin Čech ♦♦ 4.9k
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