Hmm, I narrowed down the problem some more:

For some reason Python isn't respecting the "TEMP" environment
variable so it's trying to write to /tmp on whichever node it's
running on.

I really don't understand why Python isn't respecting it.  The docs
seem to suggest it should:
http://docs.python.org/2/library/tempfile.html#tempfile.tempdir

I ran:

>qlogin
> source /usr/local/galaxy/job_environment_setup_file
> python
Python 2.7.1 (r271:86832, Apr  4 2011, 13:23:54)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tempfile
>>> tempfile.gettempdir()
'/tmp'
>>> import os
>>> os.environ['TEMP']
'/scratch/galaxy'



On Wed, Feb 6, 2013 at 3:00 PM, greg <margeem...@gmail.com> wrote:
> 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
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