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1 hg18 hg18 Human (Homo sapiens): hg18 /scratch/dongjun/galaxy/bowtie_indexes/
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2 mm9 mm9 Mouse (Mus musculus): mm9 /p/keles/SOFTWARE/bowtie-0.12.5/indexes/
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3 e_coli eschColi_536 Escherichia coli (str. 536) /p/keles/SOFTWARE/bowtie-0.12.5/indexes/
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4 e_coli_K12 eschColi_K12 Escherichia coli K12 (eschColi_K12) /scratch/dongjun/galaxy/bowtie_indexes/
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5 c_elegans_ws200 ce7 Caenorhabditis elegans (Feb 2009): WS200/ce7 /p/keles/SOFTWARE/bowtie-0.12.5/indexes/
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6 a_thaliana a_thaliana Arabidopsis thaliana /p/keles/SOFTWARE/bowtie-0.12.5/indexes/
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7
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8 #This is a sample file distributed with Galaxy that enables tools
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9 #to use a directory of Bowtie indexed sequences data files. You will
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10 #need to create these data files and then create a bowtie_indices.loc
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11 #file similar to this one (store it in this directory) that points to
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12 #the directories in which those files are stored. The bowtie_indices.loc
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13 #file has this format (longer white space characters are TAB characters):
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14 #
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15 #<unique_build_id> <dbkey> <display_name> <file_base_path>
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16 #
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17 #So, for example, if you had hg18 indexed stored in
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18 #/depot/data2/galaxy/bowtie/hg18/,
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19 #then the bowtie_indices.loc entry would look like this:
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20 #
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21 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
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22 #
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23 #and your /depot/data2/galaxy/bowtie/hg18/ directory
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24 #would contain hg18.*.ebwt files:
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25 #
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26 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
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27 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
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28 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
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29 #...etc...
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30 #
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31 #Your bowtie_indices.loc file should include an entry per line for each
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32 #index set you have stored. The "file" in the path does not actually
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33 #exist, but it is the prefix for the actual index files. For example:
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34 #
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35 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
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36 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
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37 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
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38 #...etc...
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39 #
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40 #Note that for backwards compatibility with workflows, the unique ID of
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41 #an entry must be the path that was in the original loc file, because that
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42 #is the value stored in the workflow for that parameter. That is why the
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43 #hg19 entry above looks odd. New genomes can be better-looking.
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44 #
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