diff README @ 0:10e3476429b5 draft

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+++ b/README	Fri Oct 05 13:51:49 2012 -0400
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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
+    
+    
+     
+
+