In the spirit of this solution, I've implemented something similar in -central 
changeset:

https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887fe3b4e822ba6b26b63ac3ac14bdf

The tool now creates temporary files in its working directory, which can be 
configured via the 'job_working_directory' setting; you might choose to set 
this to the same value as 'new_file_path' for simplicity.

Best,
J.


On Jul 1, 2013, at 8:32 AM, Nicolas Delhomme wrote:

> Hej Matt!
> 
> This has been bugging me as well since we are running galaxy locally with a 
> server that has a very restricted space for the /tmp directory. Here are the 
> change I made to the sam-to-bam tools to have him writing to new_file_path 
> rather than $TMP.
> 
> First in the xml file (1.1.2 is the original version of the file in the June 
> 2013 release)
> 
> delhomme:samtools$ diff sam_to_bam.xml sam_to_bam.xml_1.1.2 
> 
> 1c1
> < <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.3">
> ---
>> <tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2">
> 8d7
> <       --temp=$__app__.config.new_file_path
> 
> And in the python file:
> 
> delhomme:samtools$ diff sam_to_bam.py sam_to_bam.py_1.1.2 
> 
> 5d4
> <    --temp: hidden option to set the tmp directory
> 39d37
> <     parser.add_option( '', '--temp', dest='temp', help='The temporary 
> directory to use for writing tmp files' )
> 61d58
> <             os.remove( tmp )
> 63d59
> <             os.remove( tmp )
> 74c70
> <     tmp_dir = tempfile.mkdtemp( dir=options.temp )
> ---
>>    tmp_dir = tempfile.mkdtemp() 
> 
> 
> For the galaxy developers - I don't know if there's a way in the galaxy API 
> to do this more easily. If there's I'd love to hear about it. If not it would 
> be a great addition.
> 
> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Nathaniel Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
> 
> Tel: +46 90 786 7989
> Email: nicolas.delho...@plantphys.umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
> 
> On Apr 9, 2012, at 10:53 PM, Matt Shirley wrote:
> 
>> Is there a reason that the samtools BAM to SAM does not respect the 
>> new_file_path set in the config file? The tmp directory handling by 
>> different tool wrappers seems to be an issue right now on systems with small 
>> system tmp directories.
>> 
>> -- 
>> Matt Shirley
>> Ph.D Candidate - BCMB
>> Pevsner Lab
>> Johns Hopkins Medicine
>> 
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