diff README @ 11:6adc485b6dc0 draft default tip

Uploaded

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+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-GMAP applications and citation info are available from:    http://research-pub.gene.com/gmap/
-
-
-    Installation instructions are in the README file in the download, 
-    and online:   http://research-pub.gene.com/gmap/src/README
-
-    These tools were consistent with gmap version: 2011-11-30
-
-
-GMAP and  GSNAP use added datatypes:
-
-   add datatype definition file: lib/galaxy/datatypes/gmap.py
-
-   add the following import line to:  lib/galaxy/datatypes/registry.py
-   import gmap # added for gmap tools
-
-   add to datatypes_conf.xml
-        <!-- Start GMAP Datatypes -->
-        <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB"  display_in_upload="False"/>
-        <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex"  display_in_upload="False"/>
-        <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree"  display_in_upload="True"/>
-        <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation"  display_in_upload="False"/>
-        <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation"  display_in_upload="True"/>
-        <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation"  display_in_upload="True"/>
-        <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation"  display_in_upload="True"/>
-        <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation"  display_in_upload="True"/>
-        <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult"  display_in_upload="True"/>
-        <!-- End GMAP Datatypes -->
-
-Tools:
-  GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
-  GMAP - map sequences to a reference sequence GmapDB index
-  GSNAP - align sequences to a reference and detect splicing 
-
-  Add to  tool_conf.xml     ( probably in the "NGS: Mapping" section )
-   <tool file="gmap/gmap.xml" />
-   <tool file="gmap/gsnap.xml" />
-   <tool file="gmap/gmap_build.xml" />
-   <tool file="gmap/snpindex.xml" />
-   <tool file="gmap/iit_store.xml" />
-
-Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc
-
-
-TODO:
-  
-  
-  Add classes to gmap.py
-    CmetIndex - an index created by cmetindex
-    AtoiIndex - an index created by atoiindex
-
-  Add tally creation
-    gsnap default output -> gsnap_tally -> iit_store
-
-  Add goby support
-    Should add separate tools and datatypes for goby 
-    GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby
-
-  Possibly add Tools:
-    get_genome - retrieves from a gmapdb
-    cmetindex - create methylcytosine index
-    atoiindex - create  A-to-I RNA editing index
-    
-    
-     
-
-