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1 GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/
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2
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3
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4 Installation instructions are in the README file in the download,
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5 and online: http://research-pub.gene.com/gmap/src/README
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6
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7 These tools were consistent with gmap version: 2011-11-30
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8
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9
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10 GMAP and GSNAP use added datatypes:
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11
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12 add datatype definition file: lib/galaxy/datatypes/gmap.py
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13
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14 add the following import line to: lib/galaxy/datatypes/registry.py
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15 import gmap # added for gmap tools
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16
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17 add to datatypes_conf.xml
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18 <!-- Start GMAP Datatypes -->
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19 <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/>
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20 <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/>
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21 <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/>
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22 <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/>
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23 <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/>
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24 <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/>
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25 <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/>
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26 <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/>
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27 <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/>
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28 <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/>
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29 <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/>
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30 <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/>
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31 <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/>
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32 <!-- End GMAP Datatypes -->
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33
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34 Tools:
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35 GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations
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36 GMAP - map sequences to a reference sequence GmapDB index
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37 GSNAP - align sequences to a reference and detect splicing
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38
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39 Add to tool_conf.xml ( probably in the "NGS: Mapping" section )
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40 <tool file="gmap/gmap.xml" />
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41 <tool file="gmap/gsnap.xml" />
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42 <tool file="gmap/gmap_build.xml" />
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43 <tool file="gmap/snpindex.xml" />
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44 <tool file="gmap/iit_store.xml" />
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45
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46 Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc
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47
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48
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49 TODO:
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50
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51
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52 Add classes to gmap.py
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53 CmetIndex - an index created by cmetindex
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54 AtoiIndex - an index created by atoiindex
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55
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56 Add tally creation
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57 gsnap default output -> gsnap_tally -> iit_store
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58
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59 Add goby support
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60 Should add separate tools and datatypes for goby
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61 GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby
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62
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63 Possibly add Tools:
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64 get_genome - retrieves from a gmapdb
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65 cmetindex - create methylcytosine index
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66 atoiindex - create A-to-I RNA editing index
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67
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68
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69
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70
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71
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