On Thu, Sep 30, 2010 at 10:31 AM, Peter <peter(a)maubp.freeserve.co.uk&gt; 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.