October 2010 - galaxy-dev - lists.galaxyproject.org

Global settings from tool wrapper XML, e.g. threads
by Peter 01 Oct '10

01 Oct '10

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

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Policy on tool defaults
by Peter 01 Oct '10

01 Oct '10

Hi all, Is there an overall policy on default values when wrapping tools? e.g. Should defaults be set explicitly in the wrapper (which we can track in the Galaxy version control under hg), or omitted to let the command line tool set its own defaults? I am thinking about pipeline reproducibility as defaults can change... Peter

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SFF to (Sanger) FASTQ
by Peter 01 Oct '10

01 Oct '10

Hi all, This trivial patch makes it explicit that the sff_extract tool converts from SFF to Sanger FASTQ files: http://bitbucket.org/peterjc/galaxy-central/changeset/1c65fc26f05f I'm assuming here that datatype "fastq" in Galaxy is a legacy entry and/or only used when the FASTQ variant is unknown. Regards, Peter

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