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annotate tool-data/gmap_indices.loc.sample @ 2:52da588232b0

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Add datatypes for maps and snpindex, add iit_store and snpindex tools, update GMAP and GSNAP to use these.
author Jim Johnson <jj@umn.edu>
date Fri, 21 Oct 2011 11:38:55 -0500
parents 30d42bb409b8
children
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30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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1 #This is a sample file distributed with Galaxy that enables tools
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
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2 #to use a directory of GMAPDB indexed sequences data files. You will need
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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3 #to create these data files using gmap_build and then create a gmap_indices.loc file
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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4 #similar to this one (store it in this directory) that points to
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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5 #the directories in which those files are stored. The gmap_indices.loc
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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6 #file has this format (white space characters are TAB characters):
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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7 #
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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8 #<unique_build_id> <dbkey> <display_name> <kmers> <map,map> <snp,snp> <file_base_path>
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
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9 #hg18 hg18 hg18 (cmet atoi) 12,13,14,15 splicesites,introns snps /depot/data2/galaxy/gmap/hg18
30d42bb409b8 GMAP - add tool-data/gmap_indices.loc.sample
Jim Johnson <jj@umn.edu>
parents:
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10 #hg19 hg19 hg19 (cmet atoi) 12,13,14,15 splicesites,introns,snps snps,dbsnp /depot/data2/galaxy/gmap/hg19