Mercurial > repos > bgruening > salmonquantmerge

annotate test-data/cached_locally/salmon_indexes_versioned.loc @ 4:85b3dc9b6830 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
author bgruening
date Mon, 13 Jul 2020 17:14:25 -0400
parents 992c077f6e41
children
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43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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1 # salmon_indexes_versioned.loc.sample
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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3 # to use a directory of indexed data files. This one is for Salmon.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
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5 # First create these data files and save them in your own data directory structure.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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6 # Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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7 # Copy this file, save it with the same name (minus the .sample),
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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8 # follow the format examples, and store the result in this directory.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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9 # The file should include an one line entry for each index set.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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10 # The path points to the "basename" for the set, not a specific file.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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11 # It has four text columns seperated by TABS.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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12 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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13 # <unique_build_id> <dbkey> <display_name> <file_base_path> <version>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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14 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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15 # The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5"
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43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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19 # So, for example, if you had sacCer3 indexes stored in:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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20 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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21 # /depot/data2/galaxy/sacCer3/salmon_indexes/
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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22 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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23 # then the salmon_indexes.loc entry could look like this:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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24 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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25 #sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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26 #
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27 #More examples:
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28 #
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29 #mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4
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30 #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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31 #
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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32 #
4
85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
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33 hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q7