Global settings from tool wrapper XML, e.g. threads
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 writting, I want to set the number of threads in the XML file - again currently hard coded as 8. Peter
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 writting, 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 Othen these have comments suggesting it be modified as required for a local galaxy instance. Peter
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
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Peter