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
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