Hello,
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[1], config=sys.argv[2] )
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?
Thanks,
-Raj
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