Mercurial > repos > artbio > manta
annotate test-data/fasta_indexes.loc @ 4:d09254e37c68 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 61062db986142ec4ba86757a724bcb9b94d9f838"
| author | artbio |
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| date | Mon, 08 Jun 2020 03:11:56 -0400 |
| parents | 6a69e5d7c21f |
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| rev | line source |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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1 #This is a sample file distributed with Galaxy that enables tools |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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2 #to use a directory of Samtools indexed sequences data files. You will need |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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3 #to create these data files and then create a fasta_indexes.loc file |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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4 #similar to this one (store it in this directory) that points to |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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5 #the directories in which those files are stored. The fasta_indexes.loc |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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6 #file has this format (white space characters are TAB characters): |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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7 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
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9 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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10 #So, for example, if you had hg19 Canonical indexed stored in |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
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11 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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12 # /depot/data2/galaxy/hg19/sam/, |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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13 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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changeset
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14 #then the fasta_indexes.loc entry would look like this: |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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changeset
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15 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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17 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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18 #and your /depot/data2/galaxy/hg19/sam/ directory |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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20 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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21 #Your fasta_indexes.loc file should include an entry per line for |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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22 #each index set you have stored. The file in the path does actually |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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23 #exist, but it should never be directly used. Instead, the name serves |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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24 #as a prefix for the index file. For example: |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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changeset
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25 # |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /path/to/genome/hg18/sam_indexes/hg18canon.fa |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /path/to/genome/sam_indexes/hg18full.fa |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/sam_indexes/hg19canon.fa |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
changeset
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/sam_indexes/hg19full.fa |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
diff
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30 |
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6a69e5d7c21f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"
artbio
parents:
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31 hg19 hg19 Human hg19 ${__HERE__}/cached_locally/cached_region.fa |