Mercurial > repos > iuc > kallisto_quant

annotate tool-data/kallisto_indexes.loc.sample @ 0:59a4c97b85d6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 04:02:28 -0400
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59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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1 # kallisto_indexes.loc.sample
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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3 # to use a directory of indexed data files. This one is for kallisto.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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5 # First create these data files and save them in your own data directory structure.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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6 # Then, create a kallisto_indexes.loc file to use those indexes with tools.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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7 # Copy this file, save it with the same name (minus the .sample),
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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8 # follow the format examples, and store the result in this directory.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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9 # The file should include an one line entry for each index set.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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10 # The path points to the "basename" for the set, not a specific file.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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11 # It has four text columns seperated by TABS.
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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12 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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14 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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15 # So, for example, if you had sacCer3 indexes stored in:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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16 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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17 # /depot/data2/galaxy/sacCer3/kallisto_indexes/
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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18 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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19 # containing sacCer3 genome and sacCer3.*.ht2 files, such as:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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20 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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21 # -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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22 # -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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23 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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24 # then the kallisto_indexes.loc entry could look like this:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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25 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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26 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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27 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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28 #More examples:
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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29 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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32 #
59a4c97b85d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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33 #