diff README.rst @ 5:14561eb803a5 draft

Uploaded v3.0.1b (still working on this prior to main Tool Shed release)

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+Galaxy Wrapper for GMAP
+=======================
+
+This wrapper is copyright 2011, 2013 by Jim Johnson (Minnesota Supercomputing
+Institute, University of Minnesota).
+Revisions copyright 2016 by Peter Cock (The James Hutton Institute, UK).
+
+This Galaxy wrapper is available from the Galaxy Tool Shed at:
+
+toolshed.g2.bx.psu.edu/view/jjohnson/gmap
+
+GMAP applications and citation info are available from:
+ttp://research-pub.gene.com/gmap/
+
+Manual GMAP installation instructions are in the README file in the download,
+and online: http://research-pub.gene.com/gmap/src/README
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v2.0.0  - Initial release, for GMAP version 2011-10-07 (by JJ, October 2011).
+v2.0.1  - Updated for GMAP version 2011-11-30 (by JJ, November 2011).
+v3.0.0  - Work in progress for GMAP version 2013-05-09 (by JJ, June 2013),
+          never released to the main Galaxy Tool Shed.
+v3.0.1  - Various style updates (Peter Cock, October 2016).
+======= ======================================================================
+
+
+Automated Installation
+======================
+
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install GMAP as well.
+
+
+
+Manual Installation
+===================
+
+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