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"