Mercurial > repos > iuc > bwa_mem2

annotate tool-data/bwa_mem2_index.loc.sample @ 0:82217dccdbcf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
author iuc
date Fri, 08 Oct 2021 10:19:48 +0000
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82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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2 #to use a directory of BWA indexed sequences data files. You will need
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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3 #to create these data files and then create a bwa_index.loc file
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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4 #similar to this one (store it in this directory) that points to
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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5 #the directories in which those files are stored. The bwa_index.loc
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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6 #file has this format (longer white space characters are TAB characters):
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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7 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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8 #<unique_build_id> <dbkey> <display_name> <file_path>
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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9 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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10 #So, for example, if you had phiX indexed stored in
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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11 #/depot/data2/galaxy/phiX/base/,
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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12 #then the bwa_index.loc entry would look like this:
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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13 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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15 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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16 #and your /depot/data2/galaxy/phiX/base/ directory
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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17 #would contain phiX.fa.* files:
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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18 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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22 #...etc...
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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23 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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24 #Your bwa_index.loc file should include an entry per line for each
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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25 #index set you have stored. The "file" in the path does not actually
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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26 #exist, but it is the prefix for the actual index files. For example:
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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27 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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32 #...etc...
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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33 #
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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34 #Note that for backwards compatibility with workflows, the unique ID of
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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35 #an entry must be the path that was in the original loc file, because that
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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36 #is the value stored in the workflow for that parameter. That is why the
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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37 #hg19 entry above looks odd. New genomes can be better-looking.
82217dccdbcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 7998bbefd9bfd03bc0e92a922297b503832c0419"
iuc
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38 #