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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
author bgruening
date Tue, 02 May 2017 11:36:04 -0400
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eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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1 #This is a sample file distributed with Galaxy that enables tools
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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2 #to use a directory of Samtools indexed sequences data files. You will need
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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3 #to create these data files and then create a sam_fa_indices.loc file
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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4 #similar to this one (store it in this directory) that points to
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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5 #the directories in which those files are stored. The sam_fa_indices.loc
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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6 #file has this format (white space characters are TAB characters):
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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7 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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8 #index <seq> <location>
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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9 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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10 #So, for example, if you had hg18 indexed stored in
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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11 #/depot/data2/galaxy/sam/,
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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12 #then the sam_fa_indices.loc entry would look like this:
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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13 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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14 #index hg18 /depot/data2/galaxy/sam/hg18.fa
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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15 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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16 #and your /depot/data2/galaxy/sam/ directory
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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17 #would contain hg18.fa and hg18.fa.fai files:
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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18 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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21 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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22 #Your sam_fa_indices.loc file should include an entry per line for
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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23 #each index set you have stored. The file in the path does actually
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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24 #exist, but it should never be directly used. Instead, the name serves
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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25 #as a prefix for the index file. For example:
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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26 #
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
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27 #index hg18 /depot/data2/galaxy/sam/hg18.fa
eefd8499c801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/footprint commit 3a110c632920d1ed94b78053184978040df3edaf
bgruening
parents:
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28 #index hg19 /depot/data2/galaxy/sam/hg19.fa