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annotate tool-data/all_fasta.loc.sample @ 6:cb137e439d5d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 9fe39fd1ad0c1a5af9e8d2d633fd3e7404adbac7
author iuc
date Mon, 24 Feb 2025 13:54:25 +0000
parents 2b06e3c0bd0b
children
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2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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2 #under the "genome" directory (a directory that contains a directory
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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3 #for each build). The script extract_fasta.py will generate the file
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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5 #TAB characters):
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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6 #
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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8 #
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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9 #So, all_fasta.loc could look something like this:
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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10 #
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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14 #
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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17 #such as with hg19 above.
2b06e3c0bd0b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit dacdfa7ecfbdd1c1a12494cf7d0450185c122c84"
iuc
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18 #