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annotate tool-data/all_fasta.loc.sample @ 0:c411e2205442 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
author iuc
date Thu, 30 Apr 2020 04:05:09 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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diff changeset
2 #under the "genome" directory (a directory that contains a directory
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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diff changeset
3 #for each build). The script extract_fasta.py will generate the file
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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5 #TAB characters):
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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6 #
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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8 #
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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9 #So, all_fasta.loc could look something like this:
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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10 #
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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14 #
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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15 #Your all_fasta.loc file should contain an entry for each individual
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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16 #fasta file. So there will be multiple fasta files for each build,
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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17 #such as with hg19 above.
c411e2205442 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 41ad91410844b6d399844b253e39fa29955b96d6"
iuc
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18 #