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.delhomme(a)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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