Mercurial > repos > iuc > varscan_somatic

annotate tool-data/fasta_indexes.loc.sample @ 7:2657ab48e16a draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
author iuc
date Mon, 21 Jan 2019 12:05:00 -0500
parents 00a6be52a45a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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2 #to use a directory of Samtools indexed sequences data files. You will need
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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3 #to create these data files and then create a fasta_indexes.loc file
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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4 #similar to this one (store it in this directory) that points to
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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5 #the directories in which those files are stored. The fasta_indexes.loc
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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6 #file has this format (white space characters are TAB characters):
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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7 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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9 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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10 #So, for example, if you had hg19 Canonical indexed stored in
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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11 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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12 # /depot/data2/galaxy/hg19/sam/,
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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13 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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14 #then the fasta_indexes.loc entry would look like this:
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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15 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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17 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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20 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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21 #Your fasta_indexes.loc file should include an entry per line for
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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22 #each index set you have stored. The file in the path does actually
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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23 #exist, but it should never be directly used. Instead, the name serves
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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24 #as a prefix for the index file. For example:
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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25 #
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
00a6be52a45a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
iuc
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa