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1 #This is a sample file distributed with Galaxy that enables tools
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2 #to use a directory of Picard dict and associated files. You will need
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3 #to create these data files and then create a picard_index.loc file
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4 #similar to this one (store it in this directory) that points to
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5 #the directories in which those files are stored. The picard_index.loc
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6 #file has this format (longer white space is the TAB character):
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7 #
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8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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9 #
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10 #So, for example, if you had hg18 indexed and stored in
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11 #/depot/data2/galaxy/srma/hg18/,
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12 #then the srma_index.loc entry would look like this:
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13 #
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14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
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15 #
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16 #and your /depot/data2/galaxy/srma/hg18/ directory
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17 #would contain the following three files:
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18 #hg18.fa
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19 #hg18.dict
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20 #hg18.fa.fai
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21 #
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22 #The dictionary file for each reference (ex. hg18.dict) must be
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23 #created via Picard (http://picard.sourceforge.net). Note that
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24 #the dict file does not have the .fa extension although the
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25 #path list in the loc file does include it.
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26 #
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27 hg18 hg18 hg18 /data/galaxy/ext-tool-data/picard/hg18.fa
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28 hg19 hg19 hg19 /data/galaxy/ext-tool-data/picard/hg19.fa
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29 mm8 mm8 mm8 /data/galaxy/ext-tool-data/picard/mm8.fa
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30 mm9 mm9 mm9 /data/galaxy/ext-tool-data/picard/mm9.fa
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