Mercurial > repos > fubar > data_manager_rnasta

annotate tool-data/rnastar_index.loc.sample @ 0:84f6e67cbae5 draft

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Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
author fubar
date Mon, 29 Sep 2014 20:25:10 -0400
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84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
fubar
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1 #This is a sample file distributed with Galaxy that enables tools
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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2 #to use a directory of BWA indexed sequences data files. You will need
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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3 #to create these data files and then create a bwa_index.loc file
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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4 #similar to this one (store it in this directory) that points to
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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5 #the directories in which those files are stored. The bwa_index.loc
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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6 #file has this format (longer white space characters are TAB characters):
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7 #
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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8 #<unique_build_id> <dbkey> <display_name> <file_path>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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9 #
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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10 #So, for example, if you had phiX indexed stored in
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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11 #/depot/data2/galaxy/phiX/base/,
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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12 #then the bwa_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 #
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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16 #and your /depot/data2/galaxy/phiX/base/ directory
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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17 #would contain phiX.fa.* files:
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18 #
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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22 #...etc...
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23 #
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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24 #Your bwa_index.loc file should include an entry per line for each
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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25 #index set you have stored. The "file" in the path does not actually
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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26 #exist, but it is the prefix for the actual index files. For example:
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27 #
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28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
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29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
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30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
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31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
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32 #...etc...
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33 #
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34 #Note that for backwards compatibility with workflows, the unique ID of
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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35 #an entry must be the path that was in the original loc file, because that
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine
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36 #is the value stored in the workflow for that parameter. That is why the
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37 #hg19 entry above looks odd. New genomes can be better-looking.
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38 #