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>
line 405, in __main__
    registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] )
 line 94, in load_datatypes
    tree = galaxy.util.parse_xml( config )
 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: 

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?


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