comparison README @ 11:6adc485b6dc0 draft default tip

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author jjohnson
date Tue, 31 Jul 2012 08:19:46 -0400
parents 93911bac43da
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10:93911bac43da 11:6adc485b6dc0
1 GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/
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4 Installation instructions are in the README file in the download,
5 and online: http://research-pub.gene.com/gmap/src/README
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7 These tools were consistent with gmap version: 2011-11-30
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10 GMAP and GSNAP use added datatypes:
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12 add datatype definition file: lib/galaxy/datatypes/gmap.py
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14 add the following import line to: lib/galaxy/datatypes/registry.py
15 import gmap # added for gmap tools
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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
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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
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49 TODO:
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52 Add classes to gmap.py
53 CmetIndex - an index created by cmetindex
54 AtoiIndex - an index created by atoiindex
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56 Add tally creation
57 gsnap default output -> gsnap_tally -> iit_store
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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
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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
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