Mercurial > repos > diego > rtg_investigator
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Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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RTG Galaxy tools ---------------- Install: Copy lib/galaxy/datatypes/rtg.py and the tools/rtg directory to the same locations in your galaxy distribution. Then edit the following files: galaxy_dist/tools/rtg/rtg-galaxy.cfg change the rtg variable to point at the rtg file in your RTG installation directory galaxy_dist/lib/galaxy/datatypes/registry.py add , rtg to the list of imports beginning with data, tabular, interval... galaxy_dist/tool_conf.xml Within the <toolbox> node, add <section name="Realtime Genomics" id="rtg"> <label text="Data formatting" id="formatting" /> <tool file="rtg/format_fasta.xml" /> <tool file="rtg/format_fastq.xml" /> <tool file="rtg/cg2sdf.xml" /> <tool file="rtg/sdf2fasta.xml" /> <label text="Read mapping" id="mapping" /> <tool file="rtg/map.xml" /> <tool file="rtg/cgmap.xml" /> <tool file="rtg/mapf.xml" /> <tool file="rtg/mapx.xml" /> <label text="Variant detection" id="variant" /> <tool file="rtg/snp.xml" /> <tool file="rtg/coverage.xml" /> <tool file="rtg/snpintersection.xml" /> <label text="Simulation" id="sim" /> <tool file="rtg/genomesim.xml" /> <tool file="rtg/cgsim.xml" /> <tool file="rtg/readsim.xml" /> <tool file="rtg/snpsim.xml" /> </section> galaxy_dist/datatypes_config.xml Within the <datatypes><registration> node, add <!-- Start RTG Datatypes --> <datatype extension="rtg_sdf" type="galaxy.datatypes.rtg:Sdf"/> <datatype extension="tsvcg" type="galaxy.datatypes.rtg:Cgtsv" display_in_upload="true"/> <datatype extension="samix" type="galaxy.datatypes.rtg:Samix" display_in_upload="true"/> <!-- End RTG Datatypes --> Within the <datatypes><sniffers> node, add <sniffer type="galaxy.datatypes.rtg:Samix"/> <sniffer type="galaxy.datatypes.rtg:Cgtsv"/>