Mercurial > repos > iuc > gatk2
view gatk2_picard_index.loc.sample @ 1:f760c0de8e3a draft
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author | bgruening |
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date | Mon, 02 Dec 2013 10:36:02 -0500 |
parents | 340633249b3d |
children | 8bcc13094767 |
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#This is a sample file distributed with Galaxy that enables tools #to use a directory of Picard dict and associated files. You will need #to create these data files and then create a picard_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # #<unique_build_id> <dbkey> <display_name> <fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: #hg18.fa #hg18.dict #hg18.fa.fai # #The dictionary file for each reference (ex. hg18.dict) must be #created via Picard (http://picard.sourceforge.net). Note that #the dict file does not have the .fa extension although the #path list in the loc file does include it. # hg18 hg18 hg18 /data/galaxy/ext-tool-data/picard/hg18.fa hg19 hg19 hg19 /data/galaxy/ext-tool-data/picard/hg19.fa mm8 mm8 mm8 /data/galaxy/ext-tool-data/picard/mm8.fa mm9 mm9 mm9 /data/galaxy/ext-tool-data/picard/mm9.fa