annotate README @ 6:3be0e0a858fe

refactor and update README

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: 2011-10-16


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