Mercurial > repos > fubar > jbrowse2

annotate all_fasta.loc.sample @ 20:9c7aa5885721 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit b831bbba43ba42d44be2a91800f387fa868c7d9d
author fubar
date Tue, 30 Jan 2024 07:49:23 +0000
parents c60b17456297
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #This file lists the locations and dbkeys of all the fasta files
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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2 #under the "genome" directory (a directory that contains a directory
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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3 #for each build). The script extract_fasta.py will generate the file
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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4 #all_fasta.loc. This file has the format (white space characters are
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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5 #TAB characters):
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6 #
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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8 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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9 #So, all_fasta.loc could look something like this:
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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10 #
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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14 #
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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15 #Your all_fasta.loc file should contain an entry for each individual
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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16 #fasta file. So there will be multiple fasta files for each build,
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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17 #such as with hg19 above.
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18 #