Mercurial > repos > mvdbeek > bam_readtagger
annotate bwa_mem_index.loc.sample @ 70:f383ca1c5033 draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
author | mvdbeek |
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date | Tue, 05 Nov 2019 05:06:18 -0500 |
parents | 301316cb596a |
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301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
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2 #to use a directory of BWA indexed sequences data files. You will need |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
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3 #to create these data files and then create a bwa_index.loc file |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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4 #similar to this one (store it in this directory) that points to |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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5 #the directories in which those files are stored. The bwa_index.loc |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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6 #file has this format (longer white space characters are TAB characters): |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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7 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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8 #<unique_build_id> <dbkey> <display_name> <file_path> |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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9 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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10 #So, for example, if you had phiX indexed stored in |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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11 #/depot/data2/galaxy/phiX/base/, |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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12 #then the bwa_index.loc entry would look like this: |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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13 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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15 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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16 #and your /depot/data2/galaxy/phiX/base/ directory |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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17 #would contain phiX.fa.* files: |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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18 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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22 #...etc... |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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23 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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24 #Your bwa_index.loc file should include an entry per line for each |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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25 #index set you have stored. The "file" in the path does not actually |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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26 #exist, but it is the prefix for the actual index files. For example: |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
|
27 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
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31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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32 #...etc... |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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33 # |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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34 #Note that for backwards compatibility with workflows, the unique ID of |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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35 #an entry must be the path that was in the original loc file, because that |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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36 #is the value stored in the workflow for that parameter. That is why the |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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37 #hg19 entry above looks odd. New genomes can be better-looking. |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
parents:
diff
changeset
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38 # |