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author | Jim Johnson <jj@umn.edu> |
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date | Fri, 21 Oct 2011 12:11:45 -0500 |
parents | 52da588232b0 |
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GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/ Installation instructions are in the README file in the download, and online: http://research-pub.gene.com/gmap/src/README These galaxy tools assume gmap is configured and built with goby support. These tools were consistent with gmap version: 2011-10-07 GMAP and GSNAP use added datatypes: add datatype definition file: lib/galaxy/datatypes/gmap.py add the following import line to: lib/galaxy/datatypes/registry.py import gmap # added for gmap tools add to datatypes_conf.xml <!-- Start GMAP Datatypes --> <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> <!-- End GMAP tools --> Tools: GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations GMAP - map sequences to a reference sequence GmapDB index GSNAP - align sequences to a reference and detect splicing Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) <tool file="gmap/gmap.xml" /> <tool file="gmap/gsnap.xml" /> <tool file="gmap/gmap_build.xml" /> <tool file="gmap/snpindex.xml" /> <tool file="gmap/iit_store.xml" /> Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc TODO: Add classes to gmap.py CmetIndex - an index created by cmetindex AtoiIndex - an index created by atoiindex Possibly add Tools: get_genome - retrieves from a gmapdb cmetindex - create methylcytosine index atoiindex - create A-to-I RNA editing index