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: