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annotate tool-data/all_fasta.loc.sample @ 2:646e6943bcd2 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
author artbio
date Sun, 15 Oct 2023 12:06:24 +0000
parents c51c08cc9fcc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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1 #This file lists the locations and dbkeys of all the fasta files
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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2 #under the "genome" directory (a directory that contains a directory
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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3 #for each build). The script extract_fasta.py will generate the file
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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4 #all_fasta.loc. This file has the format (white space characters are
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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5 #TAB characters):
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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6 #
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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8 #
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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9 #So, all_fasta.loc could look something like this:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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10 #
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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14 #
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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15 #Your all_fasta.loc file should contain an entry for each individual
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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16 #fasta file. So there will be multiple fasta files for each build,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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17 #such as with hg19 above.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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18 #