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annotate tool-data/picard_index.loc.sample @ 1:e7a6416a384f draft default tip

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planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
author refinery-platform
date Mon, 04 Dec 2017 09:12:27 -0500
parents 2e42e3c01fcf
children
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2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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1 #This is a sample file distributed with Galaxy that enables tools
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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2 #to use a directory of Picard dict and associated files. You will need
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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3 #to create these data files and then create a picard_index.loc file
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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4 #similar to this one (store it in this directory) that points to
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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5 #the directories in which those files are stored. The picard_index.loc
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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6 #file has this format (longer white space is the TAB character):
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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7 #
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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8 #<unique_build_id> <dbkey> <display_name> <fasta_file_path>
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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9 #
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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10 #So, for example, if you had hg18 indexed and stored in
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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11 #/depot/data2/galaxy/srma/hg18/,
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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12 #then the srma_index.loc entry would look like this:
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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13 #
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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14 #hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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15 #
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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16 #and your /depot/data2/galaxy/srma/hg18/ directory
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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17 #would contain the following three files:
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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18 #hg18.fa
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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19 #hg18.dict
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
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20 #hg18.fa.fai
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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21 #
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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22 #The dictionary file for each reference (ex. hg18.dict) must be
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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23 #created via Picard (http://picard.sourceforge.net). Note that
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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24 #the dict file does not have the .fa extension although the
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
parents:
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25 #path list in the loc file does include it.
2e42e3c01fcf planemo upload for repository https://github.com/scottx611x/picard commit 03c50422525fa433ef6811e1dcc7e3770fabcc29-dirty
refinery-platform
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26 #