Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
annotate test-data/all_fasta.loc @ 8:3ec5c51384e6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"
author | iuc |
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date | Mon, 01 Nov 2021 08:32:15 +0000 |
parents | cc4ef4d38cf9 |
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cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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1 #This file lists the locations and dbkeys of all the fasta files |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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2 #under the "genome" directory (a directory that contains a directory |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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3 #for each build). The script extract_fasta.py will generate the file |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
diff
changeset
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4 #all_fasta.loc. This file has the format (white space characters are |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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5 #TAB characters): |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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6 # |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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7 #<unique_build_id> <dbkey> <display_name> <file_path> |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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8 # |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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9 #So, all_fasta.loc could look something like this: |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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10 # |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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14 # |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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15 #Your all_fasta.loc file should contain an entry for each individual |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build, |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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17 #such as with hg19 above. |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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18 # |
cc4ef4d38cf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents:
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19 phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |