Mercurial > repos > iuc > read_it_and_keep

annotate all_fasta.loc.sample @ 1:c271346bad2c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"
author iuc
date Thu, 17 Mar 2022 11:11:38 +0000
parents 5bad39f0703e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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2 #under the "genome" directory (a directory that contains a directory
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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3 #for each build). The script extract_fasta.py will generate the file
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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5 #TAB characters):
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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6 #
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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8 #
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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9 #So, all_fasta.loc could look something like this:
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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10 #
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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14 #
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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17 #such as with hg19 above.
5bad39f0703e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
iuc
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18 #