Mercurial > repos > nate > data_manager_bwa_mem_index_builder
annotate tool-data/bwa_mem_index.loc.sample @ 0:70543d9413d7 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
| author | nate |
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| date | Tue, 29 Jul 2025 17:14:00 +0000 |
| parents | |
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| rev | line source |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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2 #to use a directory of BWA indexed sequences data files. You will need |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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3 #to create these data files and then create a bwa_index.loc file |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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4 #similar to this one (store it in this directory) that points to |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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5 #the directories in which those files are stored. The bwa_index.loc |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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6 #file has this format (longer white space characters are TAB characters): |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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7 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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8 #<unique_build_id> <dbkey> <display_name> <file_path> |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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9 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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10 #So, for example, if you had phiX indexed stored in |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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11 #/depot/data2/galaxy/phiX/base/, |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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12 #then the bwa_index.loc entry would look like this: |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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13 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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15 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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16 #and your /depot/data2/galaxy/phiX/base/ directory |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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17 #would contain phiX.fa.* files: |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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18 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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22 #...etc... |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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23 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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24 #Your bwa_index.loc file should include an entry per line for each |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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26 #exist, but it is the prefix for the actual index files. For example: |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
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27 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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32 #...etc... |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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33 # |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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34 #Note that for backwards compatibility with workflows, the unique ID of |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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35 #an entry must be the path that was in the original loc file, because that |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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36 #is the value stored in the workflow for that parameter. That is why the |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
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37 #hg19 entry above looks odd. New genomes can be better-looking. |
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70543d9413d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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38 # |