Mercurial > repos > bgruening > hicup_truncater
annotate tool-data/bowtie2_indices.loc.sample @ 4:17f80a8600ac draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
| author | bgruening |
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| date | Fri, 25 May 2018 17:50:43 -0400 |
| parents | f413e09ae289 |
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| rev | line source |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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): |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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7 # |
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f413e09ae289
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> |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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9 # |
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f413e09ae289
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 |
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f413e09ae289
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/, |
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f413e09ae289
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: |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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13 # |
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f413e09ae289
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 |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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15 # |
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f413e09ae289
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 |
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f413e09ae289
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: |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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18 # |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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22 #...etc... |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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23 # |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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: |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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27 # |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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31 #...etc... |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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32 # |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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 |
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f413e09ae289
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. |
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f413e09ae289
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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37 # |