Mercurial > repos > jjohnson > gmap
annotate gmap/README @ 3:72ab00e732c3
Update README file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 21 Oct 2011 12:11:45 -0500 |
| parents | 52da588232b0 |
| children |
| rev | line source |
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| 3 | 1 GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/ |
| 2 | |
| 3 | |
| 4 Installation instructions are in the README file in the download, | |
| 5 and online: http://research-pub.gene.com/gmap/src/README | |
| 6 | |
| 7 These galaxy tools assume gmap is configured and built with goby support. | |
| 8 These tools were consistent with gmap version: 2011-10-07 | |
| 9 | |
| 0 | 10 |
| 11 GMAP and GSNAP use added datatypes: | |
| 12 | |
| 13 add datatype definition file: lib/galaxy/datatypes/gmap.py | |
| 14 | |
| 15 add the following import line to: lib/galaxy/datatypes/registry.py | |
| 16 import gmap # added for gmap tools | |
| 17 | |
| 18 add to datatypes_conf.xml | |
| 19 <!-- Start GMAP Datatypes --> | |
| 20 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> | |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
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21 <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
22 <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
23 <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
24 <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
25 <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
26 <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
27 <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
28 <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
29 <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
30 <!-- End GMAP tools --> |
| 0 | 31 |
| 32 Tools: | |
| 33 GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations | |
| 34 GMAP - map sequences to a reference sequence GmapDB index | |
| 35 GSNAP - align sequences to a reference and detect splicing | |
| 36 | |
| 37 Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) | |
| 38 <tool file="gmap/gmap.xml" /> | |
| 39 <tool file="gmap/gsnap.xml" /> | |
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52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
40 <tool file="gmap/gmap_build.xml" /> |
|
52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
41 <tool file="gmap/snpindex.xml" /> |
|
52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
42 <tool file="gmap/iit_store.xml" /> |
|
52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
43 |
|
52da588232b0
Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
44 Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc |
| 0 | 45 |
| 46 | |
| 47 TODO: | |
| 48 Add classes to gmap.py | |
| 49 CmetIndex - an index created by cmetindex | |
| 50 AtoiIndex - an index created by atoiindex | |
| 51 | |
| 52 Possibly add Tools: | |
| 53 get_genome - retrieves from a gmapdb | |
| 54 cmetindex - create methylcytosine index | |
| 55 atoiindex - create A-to-I RNA editing index | |
| 56 | |
| 57 | |
| 58 | |
| 59 | |
| 60 |