On Fri, Oct 1, 2010 at 3:05 PM, Peter peter@maubp.freeserve.co.uk wrote:

On Thu, Sep 30, 2010 at 10:31 AM, Peter peter@maubp.freeserve.co.uk wrote:

...

Hi all,

I'm wondering if there is any mechanism in the XML file format for tool wrappers to access global settings? e.g. something like $environment.temp to access the temp environment variable, or something like this for values in universe_wsgi.ini

http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

In particular, I'd like to know if there is a way to know how many threads a wrapped tool can use - is there a policy here?

Looking at the existing megablast wrapper, this is hard coded as 8 in the Python script, tools/metag_tools/megablast_wrapper.py For the BLAST+ wrappers I am writing, I want to set the number of threads in the XML file - again currently hard coded as 8.

Based on a quick grep and then inspection, the following tools are all hard coded to use 4 threads:

* tools/ngs_rna/cuffdiff_wrapper.xml  * tools/ngs_rna/cufflinks_wrapper.xml  * tools/ngs_rna/tophat_wrapper.xml  * tools/sr_mapping/bfast_wrapper.xml  * tools/sr_mapping/bowtie_color_wrapper.xml  * tools/sr_mapping/bowtie_wrapper.xml  * tools/sr_mapping/bwa_wrapper.xml  * tools/sr_mapping/lastz_wrapper.py

Often these have comments suggesting it be modified as required for a local galaxy instance.

How about adding another reserved parameter name, e.g. define ${GALAXY_TOOL_MAX_THREADS} for the XML wrappers?

http://bitbucket.org/peterjc/galaxy-central/changeset/05040e9891ca

Note that this change needs real testing before committing to the main repository - I don't have all the required tools installed locally.

Peter