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: