In the spirit of this solution, I've implemented something similar in -central changeset: https://bitbucket.org/galaxy/galaxy-central/commits/c7a07f350887fe3b4e822ba6... 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.delhomme@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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