Mercurial > repos > diego > rtg_investigator
diff README @ 1:8593828f91e7 default tip
Full galaxy wrapper
| author | diego |
|---|---|
| date | Sat, 21 Apr 2012 21:36:15 -0400 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Sat Apr 21 21:36:15 2012 -0400 @@ -0,0 +1,56 @@ +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"/>