annotate test-data/all_fasta.loc @ 1:05693c942b1a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:54:59 +0000
parents 19c6d9c66c75
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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2 #under the "genome" directory (a directory that contains a directory
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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3 #for each build). The script extract_fasta.py will generate the file
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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4 #all_fasta.loc. This file has the format (white space characters are
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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5 #TAB characters):
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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6 #
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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8 #
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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9 #So, all_fasta.loc could look something like this:
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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10 #
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
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14 #
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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17 #such as with hg19 above.
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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18 #
19c6d9c66c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_dnaprints commit 91c7f7c66a4dcbf3d0074f3a49a1a536aea70663"
iuc
parents:
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19 AF2122 AF2122 AF2122 ${__HERE__}/AF2122.fa