Mercurial > repos > jjohnson > gmap
comparison README @ 6:3be0e0a858fe
refactor and update README
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 08 Nov 2011 13:22:34 -0600 |
| parents | |
| children | 7f032685214b |
comparison
equal
deleted
inserted
replaced
| 5:f4b4c1712e39 | 6:3be0e0a858fe |
|---|---|
| 1 GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/ | |
| 2 | |
| 3 | |
| 4 Installation instructions are in the README file in the download, | |
| 5 and online: http://research-pub.gene.com/gmap/src/README | |
| 6 | |
| 7 These tools were consistent with gmap version: 2011-10-16 | |
| 8 | |
| 9 | |
| 10 GMAP and GSNAP use added datatypes: | |
| 11 | |
| 12 add datatype definition file: lib/galaxy/datatypes/gmap.py | |
| 13 | |
| 14 add the following import line to: lib/galaxy/datatypes/registry.py | |
| 15 import gmap # added for gmap tools | |
| 16 | |
| 17 add to datatypes_conf.xml | |
| 18 <!-- Start GMAP Datatypes --> | |
| 19 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> | |
| 20 <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> | |
| 21 <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> | |
| 22 <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> | |
| 23 <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> | |
| 24 <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> | |
| 25 <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/> | |
| 26 <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> | |
| 27 <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> | |
| 28 <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> | |
| 29 <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> | |
| 30 <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/> | |
| 31 <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/> | |
| 32 <!-- End GMAP Datatypes --> | |
| 33 | |
| 34 Tools: | |
| 35 GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations | |
| 36 GMAP - map sequences to a reference sequence GmapDB index | |
| 37 GSNAP - align sequences to a reference and detect splicing | |
| 38 | |
| 39 Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) | |
| 40 <tool file="gmap/gmap.xml" /> | |
| 41 <tool file="gmap/gsnap.xml" /> | |
| 42 <tool file="gmap/gmap_build.xml" /> | |
| 43 <tool file="gmap/snpindex.xml" /> | |
| 44 <tool file="gmap/iit_store.xml" /> | |
| 45 | |
| 46 Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc | |
| 47 | |
| 48 | |
| 49 TODO: | |
| 50 | |
| 51 | |
| 52 Add classes to gmap.py | |
| 53 CmetIndex - an index created by cmetindex | |
| 54 AtoiIndex - an index created by atoiindex | |
| 55 | |
| 56 Add tally creation | |
| 57 gsnap default output -> gsnap_tally -> iit_store | |
| 58 | |
| 59 Add goby support | |
| 60 Should add separate tools and datatypes for goby | |
| 61 GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby | |
| 62 | |
| 63 Possibly add Tools: | |
| 64 get_genome - retrieves from a gmapdb | |
| 65 cmetindex - create methylcytosine index | |
| 66 atoiindex - create A-to-I RNA editing index | |
| 67 | |
| 68 | |
| 69 | |
| 70 | |
| 71 |