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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 vcf file for covacs sequences data files. You will need
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3 #to create these data files and then create a vcf_loc.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 vcf_loc.loc
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6 #file has this format (longer white space characters are TAB characters):
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7 #
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8 #<unique_id> <display_name> <file_path>
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9 #
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10 #So, for example, if you had vcf file stored in
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11 #/export/resource/,
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12 #then the covacs_vcf.loc entry would look like this:
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13 #
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14 #hapmap hapmap /export/resource/hapmap.vcf
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15 #
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16 #and your /export/resource directory
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17 #would contain hapmap.vcf.
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18 #
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19 #
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20 #Your covacs_vcf.loc file should include an entry per line for each
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21 #index set you have stored. The "file" in the path does not actually
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22 #exist, but it is the prefix for the actual index files.
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23 #Note that for backwards compatibility with workflows, the unique ID of
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24 #an entry must be the path that was in the original loc file, because that
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25 #is the value stored in the workflow for that parameter.
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26 #
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27 hapmap hapmap /export/resources/hapmap.vcf
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28 1000G 1000G /export/resources/1000G.vcf
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