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annotate tool-data/picard_index.loc.sample @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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1 #This is a sample file distributed with Galaxy that enables tools
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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2 #to use a directory of Picard dict and associated files. You will need
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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3 #to create these data files and then create a picard_index.loc file
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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4 #similar to this one (store it in this directory) that points to
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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5 #the directories in which those files are stored. The picard_index.loc
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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6 #file has this format (longer white space is the TAB character):
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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7 #
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path>
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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9 #
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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10 #So, for example, if you had hg18 indexed and stored in
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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11 #/depot/data2/galaxy/srma/hg18/,
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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12 #then the srma_index.loc entry would look like this:
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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13 #
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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15 #
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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16 #and your /depot/data2/galaxy/srma/hg18/ directory
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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17 #would contain the following three files:
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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18 #hg18.fa
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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19 #hg18.dict
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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20 #hg18.fa.fai
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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21 #
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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22 #The dictionary file for each reference (ex. hg18.dict) must be
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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23 #created via Picard (http://picard.sourceforge.net). Note that
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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24 #the dict file does not have the .fa extension although the
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
parents:
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25 #path list in the loc file does include it.
b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
avowinkel
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26 #