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annotate tool-data/all_fasta.loc.sample @ 10:8711df965d4b draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
author artbio
date Wed, 24 Jan 2024 19:26:57 +0000
parents 41e68da5c0fe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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1 #This file lists the locations and dbkeys of all the fasta files
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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2 #under the "genome" directory (a directory that contains a directory
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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3 #for each build). The script extract_fasta.py will generate the file
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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4 #all_fasta.loc. This file has the format (white space characters are
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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5 #TAB characters):
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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6 #
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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8 #
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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9 #So, all_fasta.loc could look something like this:
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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10 #
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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14 #
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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15 #Your all_fasta.loc file should contain an entry for each individual
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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16 #fasta file. So there will be multiple fasta files for each build,
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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17 #such as with hg19 above.
41e68da5c0fe "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51517e64f8536c5a3192b00a1fa39d5b8cf3a954"
artbio
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18 #