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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 Smalt indexed sequences data files. You will need
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3 #to create these data files and then create a smalt_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 smalt_index.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_build_id> <dbkey> <display_name> <file_path>
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9 #
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10 #So, for example, if you had phiX indexed stored in
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11 #/depot/data2/galaxy/phiX/base/,
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12 #then the smalt_index.loc entry would look like this:
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13 #
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14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
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15 #
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16 #and your /depot/data2/galaxy/phiX/base/ directory
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17 #would contain hg19.fa.* files:
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18 #
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19 #-rw-r--r-- 1 cborroto universe 527388 2005-09-13 10:12 phix.fa.sma
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20 #-rw-r--r-- 1 cborroto universe 269808 2005-09-13 10:12 phiX.fa.smi
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21 #
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22 #Your smalt_index.loc file should include an entry per line for each
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23 #index set you have stored. The "file" in the path does not actually
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24 #exist, but it is the prefix for the actual index files. For example:
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25 #
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26 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
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27 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
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28 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
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