On Fri, Oct 1, 2010 at 3:05 PM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
On Thu, Sep 30, 2010 at 10:31 AM, Peter
<peter(a)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