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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