Mercurial > repos > diego > rtg_investigator
comparison README @ 1:8593828f91e7 default tip
Full galaxy wrapper
| author | diego |
|---|---|
| date | Sat, 21 Apr 2012 21:36:15 -0400 |
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| 0:d50638ebd809 | 1:8593828f91e7 |
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| 1 RTG Galaxy tools | |
| 2 ---------------- | |
| 3 | |
| 4 Install: | |
| 5 | |
| 6 Copy lib/galaxy/datatypes/rtg.py and the tools/rtg directory to the same locations in your galaxy distribution. | |
| 7 | |
| 8 Then edit the following files: | |
| 9 | |
| 10 galaxy_dist/tools/rtg/rtg-galaxy.cfg | |
| 11 | |
| 12 change the rtg variable to point at the rtg file in your RTG installation directory | |
| 13 | |
| 14 galaxy_dist/lib/galaxy/datatypes/registry.py | |
| 15 add | |
| 16 , rtg | |
| 17 to the list of imports beginning with data, tabular, interval... | |
| 18 | |
| 19 | |
| 20 galaxy_dist/tool_conf.xml | |
| 21 Within the <toolbox> node, add | |
| 22 | |
| 23 <section name="Realtime Genomics" id="rtg"> | |
| 24 <label text="Data formatting" id="formatting" /> | |
| 25 <tool file="rtg/format_fasta.xml" /> | |
| 26 <tool file="rtg/format_fastq.xml" /> | |
| 27 <tool file="rtg/cg2sdf.xml" /> | |
| 28 <tool file="rtg/sdf2fasta.xml" /> | |
| 29 <label text="Read mapping" id="mapping" /> | |
| 30 <tool file="rtg/map.xml" /> | |
| 31 <tool file="rtg/cgmap.xml" /> | |
| 32 <tool file="rtg/mapf.xml" /> | |
| 33 <tool file="rtg/mapx.xml" /> | |
| 34 <label text="Variant detection" id="variant" /> | |
| 35 <tool file="rtg/snp.xml" /> | |
| 36 <tool file="rtg/coverage.xml" /> | |
| 37 <tool file="rtg/snpintersection.xml" /> | |
| 38 <label text="Simulation" id="sim" /> | |
| 39 <tool file="rtg/genomesim.xml" /> | |
| 40 <tool file="rtg/cgsim.xml" /> | |
| 41 <tool file="rtg/readsim.xml" /> | |
| 42 <tool file="rtg/snpsim.xml" /> | |
| 43 </section> | |
| 44 | |
| 45 galaxy_dist/datatypes_config.xml | |
| 46 Within the <datatypes><registration> node, add | |
| 47 | |
| 48 <!-- Start RTG Datatypes --> | |
| 49 <datatype extension="rtg_sdf" type="galaxy.datatypes.rtg:Sdf"/> | |
| 50 <datatype extension="tsvcg" type="galaxy.datatypes.rtg:Cgtsv" display_in_upload="true"/> | |
| 51 <datatype extension="samix" type="galaxy.datatypes.rtg:Samix" display_in_upload="true"/> | |
| 52 <!-- End RTG Datatypes --> | |
| 53 | |
| 54 Within the <datatypes><sniffers> node, add | |
| 55 <sniffer type="galaxy.datatypes.rtg:Samix"/> | |
| 56 <sniffer type="galaxy.datatypes.rtg:Cgtsv"/> |