Hi Nate,

I don't see $TMPDIR being set on the cluster, in addition to my
previous email I ran:

>>> print os.environ.keys()
['KDE_IS_PRELINKED', 'FACTERLIB', 'LESSOPEN', 'SGE_CELL', 'LOGNAME',
'USER', 'INPUTRC', 'QTDIR', 'PATH', 'PS1', 'LANG', 'KDEDIR', 'TERM',
'SHELL', 'TEMP', 'QTINC', 'G_BROKEN_FILENAMES', 'SGE_EXECD_PORT',
'HISTSIZE', 'KDE_NO_IPV6', 'MANPATH', 'HOME', 'SGE_ROOT', 'QTLIB',
'VIRTUAL_ENV', 'SGE_CLUSTER_NAME', '_', 'SSH_CONNECTION', 'SSH_TTY',
'HOSTNAME', 'SSH_CLIENT', 'SHLVL', 'PWD', 'MAIL', 'LS_COLORS',
'SGE_QMASTER_PORT']

But I think we've narrowed it down to something interfering with
Python deciding the temp file location.  I just can't figure out what.



On Wed, Feb 6, 2013 at 3:18 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Feb 6, 2013, at 3:00 PM, greg 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?
>
> Hi Greg,
>
> The first place to look would be in lib/galaxy/datatypes/sniff.py, line 96:
>
>     fd, temp_name = tempfile.mkstemp()
>
> If you print temp_name, that will tell you what file the upload tool is 
> writing to.  You may also want to take a look at:
>
>     http://docs.python.org/2/library/tempfile.html#tempfile.tempdir
>
> Some cluster environments set $TMPDIR, and if that is set, $TEMP will not be 
> used.
>
> --nate
>
>>
>> -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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>
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