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 <[email protected]
<mailto:[email protected]>> 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
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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: [email protected]
Skype: live:clinton.chee
Twitter: @xtechnotes <https://twitter.com/xtechnotes>
PBSWorks: Facebook <https://www.facebook.com/pbsworks> | Google+
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Australia Toll Free: 1800 174 396
Urgent / Emergency: [email protected]
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*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: [email protected]
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: [email protected]
___________________________________________________________
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in your mail client. To manage your subscriptions to this
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