[galaxy-dev] Running Jobs:

13 Aug 2013

      Hey All,

Apologies for all the questions on the mailing list...I am having a lot of
difficulty getting our local Galaxy working.

Currently I have galaxy running but when I try run a job it just stays on
"Job is waiting to run" and never runs.

I have read the guide and wiki but can't seem to solve my problem at all...

The output of sh run.sh:

sh run.sh
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
  from csamtools import *
python path is:
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/boto-2.5.2-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Whoosh-0.3.18-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/amqplib-0.6.1-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/pexpect-2.4-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Babel-0.9.4-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Mako-0.4.1-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebHelpers-0.2-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/WebOb-0.8.5-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Routes-1.12.3-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/wchartype-0.1-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/docutils-0.7-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/PasteDeploy-1.5.0-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/Paste-1.7.5.1-py2.6.egg,
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/lib,
/scratch/sysusers/galaxy/galaxy_env/lib64/python26.zip,
/scratch/sysusers/galaxy/galaxy_env/lib64/python2.6,
/scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/plat-linux2,
/scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-tk,
/scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-old,
/scratch/sysusers/galaxy/galaxy_env/lib64/python2.6/lib-dynload,
/usr/lib64/python2.6, /usr/lib/python2.6,
/scratch/sysusers/galaxy/galaxy_env/lib/python2.6/site-packages
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105:
SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed
from 'postgres' to 'postgresql'. The new URL format is
postgresql[+driver]://<user>:<pass>@<host>/<dbname>
Starting server in PID 59419.
serving on 0.0.0.0:8989 view at http://127.0.0.1:8989
/scratch/sysusers/galaxy/galaxy-galaxy-dist-ebe87051fadf/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/expression.py:1927:
SAWarning: The IN-predicate on "request_type.id" was invoked with an empty
sequence. This results in a contradiction, which nonetheless can be
expensive to evaluate.  Consider alternative strategies for improved
performance.
155.240.187.100 - - [13/Aug/2013:12:28:36 +0000] "GET /root HTTP/1.1" 200 -
"-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101
Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /root/welcome
HTTP/1.1" 302 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET /history HTTP/1.1"
200 - "http://155.240.187.2:8989/root" "Mozilla/5.0 (Macintosh; Intel Mac
OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:28:37 +0000] "GET
/history/get_display_application_links HTTP/1.1" 200 - "
http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X
10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "POST /tool_runner
HTTP/1.1" 200 - "http://genome.ucsc.edu/cgi-bin/hgTables" "Mozilla/5.0
(Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:32:30 +0000] "GET /history HTTP/1.1"
200 - "http://155.240.187.2:8989/tool_runner" "Mozilla/5.0 (Macintosh;
Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET
/api/histories/f597429621d6eb2b HTTP/1.1" 200 - "
http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X
10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:32:31 +0000] "GET
/history/get_display_application_links HTTP/1.1" 200 - "
http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X
10.8; rv:22.0) Gecko/20100101 Firefox/22.0"
155.240.187.100 - - [13/Aug/2013:12:32:35 +0000] "GET
/api/histories/f597429621d6eb2b HTTP/1.1" 200 - "
http://155.240.187.2:8989/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X
10.8; rv:22.0) Gecko/20100101 Firefox/22.0"

I would I check to see if a job is passed on to torque via drmaa?

Any help would be appreciated

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin