Hi Nate,

Also, the only configuration I did on my Galaxy installation is the job_conf.xml file. I have not edited any of the other xml files or used other config sample files.
Should I also have edited some other XML configuration files.

Also, do I need to have run any of the executbales in the main directory, besides ./run.sh?



The list of files in config/ is:
[galaxy_user@bio config]$ ls -latrF
total 312
-rw-rw-r-- 1 galaxy_user galaxy_user 416 Sep 3 10:42 disposable_email_blacklist.conf.sample -rw-rw-r-- 1 galaxy_user galaxy_user 44878 Sep 3 10:42 datatypes_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4444 Sep 3 10:42 auth_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 234 Sep 3 10:42 external_service_types_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user 48599 Sep  3 10:42 galaxy.ini.sample
-rw-rw-r-- 1 galaxy_user galaxy_user 463 Sep 3 10:42 job_conf.xml.sample_basic -rw-rw-r-- 1 galaxy_user galaxy_user 30390 Sep 3 10:42 job_conf.xml.sample_advanced -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:42 migrated_tools_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 725 Sep 3 10:42 job_resource_params_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 6728 Sep 3 10:42 job_metrics_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 220 Sep 3 10:42 openid_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 2165 Sep 3 10:42 object_store_conf.xml.sample
drwxrwxr-x  4 galaxy_user galaxy_user  4096 Sep  3 10:42 plugins/
-rw-rw-r-- 1 galaxy_user galaxy_user 69 Sep 3 10:42 shed_tool_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:42 shed_data_manager_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3139 Sep 3 10:42 reports_wsgi.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 288 Sep 3 10:42 tool_sheds_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 5552 Sep 3 10:42 tool_shed.ini.sample -rw-rw-r-- 1 galaxy_user galaxy_user 3273 Sep 3 10:42 tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 4925 Sep 3 10:42 tool_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user  5840 Sep  3 10:42 tool_conf.xml.main
-rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:42 shed_tool_data_table_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 548 Sep 3 10:42 workflow_schedulers_conf.xml.sample -rw-rw-r-- 1 galaxy_user galaxy_user 68 Sep 3 10:52 migrated_tools_conf.xml
-rw-rw-r--  1 galaxy_user galaxy_user    69 Sep  3 10:52 shed_tool_conf.xml
-rw-rw-r-- 1 galaxy_user galaxy_user 41 Sep 3 10:52 shed_tool_data_table_conf.xml -rw-rw-r-- 1 galaxy_user galaxy_user 55 Sep 3 10:52 shed_data_manager_conf.xml
-rw-------  1 root        root            0 Sep  4 17:12 STDIN.o2
-rw-------  1 root        root            0 Sep  4 17:12 STDIN.e2
-rw-rw-r--  1 galaxy_user galaxy_user   512 Sep  4 22:11 job_conf.xml.sample
-rw-rw-r--  1 galaxy_user galaxy_user 48599 Sep  4 22:42 galaxy.ini
-rw-rw-r--  1 galaxy_user galaxy_user   631 Sep  7 14:48 job_conf.xmlDRA
-rw-r--r--  1 galaxy_user galaxy_user   909 Sep 14 16:20 job_conf.xml
drwxrwxr-x  3 galaxy_user galaxy_user  4096 Sep 14 16:23 ./
drwxrwxr-x 24 galaxy_user galaxy_user  4096 Sep 14 16:27 ../

On 14/09/2015 4:22 PM, Clinton Chee wrote:
Hi Nate,

I was trying the Galaxy configuration using the tips you suggested - I think I got one step ahead, but stuck again.
Now  the job status says "waiting to run"

I got a screenshot attached - focussing on job 42 - which is a Sort job using a dataset I downloaded. Please note, I am setting up Galaxy, but I am not a bioinfomatics person. I'm a PBS person and need to use DRMAA - and I'm not sure how else to debug this.

Below is the job_conf.xml - I've also tried the hostname apart from localhost.

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no expl
icit config). -->
<job_conf>
    <plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
    </plugins>
    <handlers default="localhost">
        <handler id="localhost"/>
    </handlers>
    <destinations default="drmaa">
        <destination id="local" runner="local"/>
        <destination id="drmaa" runner="drmaa">
                <param id="nativeSpecification">-q workq@localhost</param>
        </destination>
    </destinations>
</job_conf>


Thanks
Clinton

On 9/09/2015 4:44 AM, Nate Coraor wrote:
Hi Clinton,

On Mon, Sep 7, 2015 at 2:23 AM, Clinton Chee <c...@altair.com <mailto:c...@altair.com>> wrote:

    Dear Galaxy devs / support,

    I am trying to understand the following snippet from job_conf.xml
    (I want to use drmaa v1)
    ------------
    <destination id="pbs_drmaa_orion" runner="drmaa" tags="merc">
                <param id="destination">galaxy@merc</param>
     </destination>
    ------------


    Based on someone's configuration above, I am trying to customize
    to my system.

    I'm trying to understand where/how the parameters are associated?
    - tags?


Tags are identifiers used to map tools to destinations. You probably do not need to use them, but if you wanted to have a tool (or the default destination) send jobs to more than one destination (selected at random), tags are used for that. They can also be used for setting job concurrency limits.

    - destination in param id? is this the queue?  I also checked the
    DRMAA specification but cannot find any "destination" as a keyword.


I am not sure where this example came from but I don't believe it would work - the "destination" param works with the "pbs" runner, but the pbs runner only works with Torque, as far as I know. The drmaa runner expects params that conform to the DRMAA specification, the most common of which is `nativeSpecification`. If you wanted to set the destination for PBS Pro using the drmaa runner, the param would be:

    <param id="nativeSpecification">-q queue@server_name</param>

    - galaxy@merc?   is merc pointing to the hostname, and galaxy the
    queue name? (I know the instution's cluster is called "merc", but
    I don't know if the "merc" in the tag is for convenience or is
    being read as the hostname?


That format is a PBS destination identifier, so `galaxy` is the queue on the PBS server `merc`.
Hope this helps, please let us know if this doesn't clear things up.

--nate



    I've looked through:
    https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
    https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
    https://wiki.galaxyproject.org/Admin/Config/Jobs - describes
    job_conf.xml

    but cannot make sense, eg. for "tags" is says "Tags to which this
    destination belongs."
    Eg. "tags="longwalltime,bigcluster""


    Do you have more detailed documention on configuration?

    Thanks
    Clinton


-- ------------------------------------------------------------------------
    *PBS WorksTM named #1 software product!*
    HPCwire Reader’s Choice Awards 2014
    *
    For more information on Altair’s award-winning HPC
    workload management suite, please visit pbsworks.com
    <http://pbsworks.com/> *
    ------------------------------------------------------------------------
    Clinton Chee (PhD)
    PBS Application Engineer
    Altair - Innovation Intelligence
    Mob: 61 (0)402 058 983
    Email: c...@altair.com <mailto:c...@altair.com>
    Skype: live:clinton.chee
    Twitter: @xtechnotes
    <https://twitter.com/xtechnotes>!function(d,s,id){var
    
js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id))
    
<http:/.test%28d.location%29?%27http%27:%27https%27;if%28%21d.getElementById%28id%29%29>{js=d.createElement(s);js.id
    
<http://js.id>=id;js.src=p+'://platform.twitter.com/widgets.js';fjs.parentNode.insertBefore
    
<http://platform.twitter.com/widgets.js%27;fjs.parentNode.insertBefore>(js,fjs);}}(document,
    'script', 'twitter-wjs');
    PBSWorks: Facebook <https://www.facebook.com/pbsworks>| Google+
    <https://plus.google.com/116621495421190215237>| Linkedin
    <http://www.linkedin.com/groups?gid=2112011> | Twitter
    <https://twitter.com/PBSWorks>| YouTube
    <http://www.youtube.com/thepbsworks>
    Australia Toll Free: 1800 174 396
    Urgent / Emergency:
    <mailto:pbs-supp...@india.altair.com>pbs-supp...@india.altair.com




    ___________________________________________________________
    Please keep all replies on the list by using "reply all"
    in your mail client.  To manage your subscriptions to this
    and other Galaxy lists, please use the interface at:
    https://lists.galaxyproject.org/

    To search Galaxy mailing lists use the unified search at:
    http://galaxyproject.org/search/mailinglists/




--
------------------------------------------------------------------------
*PBS WorksTM named #1 software product!*
HPCwire Reader’s Choice Awards 2014
*
For more information on Altair’s award-winning HPC
workload management suite, please visit pbsworks.com <http://pbsworks.com> *
------------------------------------------------------------------------
Clinton Chee (PhD)
PBS Application Engineer
Altair - Innovation Intelligence
Mob: 61 (0)402 058 983
Email: c...@altair.com
Skype: live:clinton.chee
Twitter: @xtechnotes <https://twitter.com/xtechnotes>
PBSWorks: Facebook <https://www.facebook.com/pbsworks> | Google+ <https://plus.google.com/116621495421190215237> | Linkedin <http://www.linkedin.com/groups?gid=2112011> | Twitter <https://twitter.com/PBSWorks> | YouTube <http://www.youtube.com/thepbsworks>
Australia Toll Free: 1800 174 396
Urgent / Emergency: pbs-supp...@india.altair.com


--
------------------------------------------------------------------------
*PBS WorksTM named #1 software product!*
HPCwire Reader’s Choice Awards 2014
*
For more information on Altair’s award-winning HPC
workload management suite, please visit pbsworks.com <http://pbsworks.com> *
------------------------------------------------------------------------
Clinton Chee (PhD)
PBS Application Engineer
Altair - Innovation Intelligence
Mob: 61 (0)402 058 983
Email: c...@altair.com
Skype: live:clinton.chee
Twitter: @xtechnotes <https://twitter.com/xtechnotes>
PBSWorks: Facebook <https://www.facebook.com/pbsworks> | Google+ <https://plus.google.com/116621495421190215237> | Linkedin <http://www.linkedin.com/groups?gid=2112011> | Twitter <https://twitter.com/PBSWorks> | YouTube <http://www.youtube.com/thepbsworks>
Australia Toll Free: 1800 174 396
Urgent / Emergency: pbs-supp...@india.altair.com
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to