I am setting up a new instance of Galaxy (based on the latest dev branch on github repo) configured to submit the jobs to a remote cluster via pulsar. I used the usegalaxy playbook to get the configuration parameters for the galaxy job_conf.xml and pulsar app.yml files. I was partially successful in running the jobs via pulsar, the regular tools (analysis tools, etc..) are running OK on the remote cluster. I am having trouble getting the upload tool to run on the the remote cluster.
Here is the error I see in the galaxy error report for the job: It looks like the upload tool running on the remote machine is trying to access a file in the database/tmp area of the galaxy server machine.
Traceback (most recent call last): File "/escratch4/apps/galaxy_scratch/pulsar/files/staging/46/tool_files/upload.py", line 430, in <module> __main__() File "/escratch4/apps/galaxy_scratch/pulsar/files/staging/46/tool_files/upload.py", line 405, in __main__ registry.load_datatypes( root_dir=sys.argv, config=sys.argv ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy/lib/galaxy/datatypes/registry.py", line 94, in load_datatypes tree = galaxy.util.parse_xml( config ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy/lib/galaxy/util/__init__.py", line 178, in parse_xml root = tree.parse( fname, parser=ElementTree.XMLParser( target=DoctypeSafeCallbackTarget() ) ) File "/usr/local/python/2.7.8/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/home/galaxy/wkdir/galaxy/database/tmp/tmpp6j83l'
I've created a Gist with the contents of job_conf.xml, app.yml, file action file, error content at https://gist.github.com/raj76/7be86f6a56714deef050 .
Any suggestions on how to debug this issue?