Mercurial > repos > artbio > small_read_size_histograms
annotate tool-data/bowtie_indices.loc.sample @ 1:dce695815b0f draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit 87fad8a906abdb9dc2ecaa2457fb26ab2b09895d
| author | artbio |
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| date | Tue, 11 Jul 2017 13:10:00 -0400 |
| parents | 234b83159ea8 |
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| rev | line source |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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2 #to use a directory of Bowtie indexed sequences data files. You will |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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3 #need to create these data files and then create a bowtie_indices.loc |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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4 #file similar to this one (store it in this directory) that points to |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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5 #the directories in which those files are stored. The bowtie_indices.loc |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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6 #file has this format (longer white space characters are TAB characters): |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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7 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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8 #<unique_build_id> <dbkey> <display_name> <file_base_path> |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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9 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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10 #So, for example, if you had hg18 indexed stored in |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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11 #/depot/data2/galaxy/bowtie/hg18/, |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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12 #then the bowtie_indices.loc entry would look like this: |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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13 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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15 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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16 #and your /depot/data2/galaxy/bowtie/hg18/ directory |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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17 #would contain hg18.*.ebwt files: |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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18 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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22 #...etc... |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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23 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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24 #Your bowtie_indices.loc file should include an entry per line for each |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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25 #index set you have stored. The "file" in the path does not actually |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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26 #exist, but it is the prefix for the actual index files. For example: |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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27 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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changeset
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28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
changeset
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30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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31 #...etc... |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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32 # |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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33 #Note that for backwards compatibility with workflows, the unique ID of |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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34 #an entry must be the path that was in the original loc file, because that |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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35 #is the value stored in the workflow for that parameter. That is why the |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff
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36 #hg19 entry above looks odd. New genomes can be better-looking. |
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234b83159ea8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
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37 # |