Thanks Nate, It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy But when I look in that directory, there's plenty of free space, and I also don't see any recent files there. So I'm wondering if the upload jobs aren't seeing that for some reason. Any ideas on how I could diagnose this more? -Greg Relevant info? >grep env galaxy-dist/universe_wsgi.ini environment_setup_file = /usr/local/galaxy/job_environment_setup_file >cat /usr/local/galaxy/job_environment_setup_file export TEMP=/scratch/galaxy #active Python virtual env just for galaxy source /usr/local/galaxy/galaxy_python/bin/activate ... path setup lines ... On Wed, Feb 6, 2013 at 2:37 PM, Nate Coraor <n...@bx.psu.edu> wrote: > On Feb 6, 2013, at 2:32 PM, greg wrote: > >> Hi guys, >> >> When I try to upload a directory of files from a server directory I'm >> seeing the error below. >> >> It appears to be trying to write to a temp directory somewhere that >> I'm guessing doesn't have enough space? Is there a way I can direct >> where it writes to for temporary files like this? > > Hi Greg, > > There are a few ways. For some parts of Galaxy, you will want to set > new_file_path in universe_wsgi.ini to a suitable temp space. However, this > is not the case for the upload tool. > >> Am I understanding right, that these upload jobs are running on our >> cluster? I think it would be a problem if its trying to use the >> default temp directory on each cluster node since they aren't >> provisioned with much space. > > This is correct. On the cluster, add something to your user's shell startup > files (or see the environment_setup_file option in universe_wsgi.ini) that > will set the $TEMP or $TMPDIR environment variable to a suitable temp space. > > --nate > >> >> Please advise. >> >> Thanks, >> >> Greg >> >> >> >> Miscellaneous information:Traceback (most recent call last): File >> "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line >> 384, in __main__() File >> "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line >> 373, in __main__ add_file( dataset, >> Job Standard Error >> >> >> Traceback (most recent call last): >> File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", >> line 384, in >> __main__() >> File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", >> line 373, in __main__ >> add_file( dataset, registry, json_file, output_path ) >> File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", >> line 270, in add_file >> line_count, converted_path = sniff.convert_newlines( dataset.path, >> in_place=in_place ) >> File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py", >> line 99, in convert_newlines >> fp.write( "%s\n" % line.rstrip( "\r\n" ) ) >> IOError: [Errno 28] No space left on device >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
