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annotate tool-data/bowtie2_indices.loc.sample @ 5:2edfb71706b3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author bgruening
date Sat, 22 Oct 2022 08:41:11 +0000
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a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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1 #This is a sample file distributed with Galaxy that enables tools
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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2 #to use a directory of Bowtie2 indexed sequences data files. You will
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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3 #need to create these data files and then create a bowtie_indices.loc
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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4 #file similar to this one (store it in this directory) that points to
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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5 #the directories in which those files are stored. The bowtie2_indices.loc
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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6 #file has this format (longer white space characters are TAB characters):
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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7 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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9 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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10 #So, for example, if you had hg18 indexed stored in
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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11 #/depot/data2/galaxy/bowtie2/hg18/,
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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12 #then the bowtie2_indices.loc entry would look like this:
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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13 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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15 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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16 #and your /depot/data2/galaxy/bowtie2/hg18/ directory
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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17 #would contain hg18.*.ebwt files:
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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18 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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22 #...etc...
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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23 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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24 #Your bowtie2_indices.loc file should include an entry per line for each
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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25 #index set you have stored. The "file" in the path does not actually
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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26 #exist, but it is the prefix for the actual index files. For example:
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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27 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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31 #...etc...
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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32 #
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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33 #Note that for backwards compatibility with workflows, the unique ID of
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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34 #an entry must be the path that was in the original loc file, because that
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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35 #is the value stored in the workflow for that parameter. That is why the
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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36 #hg19 entry above looks odd. New genomes can be better-looking.
a47a96d2721a planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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37 #