Mercurial > repos > diego > rtg_investigator
comparison README @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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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"/> |