Mercurial > repos > iuc > data_manager_bwameth_index_builder
annotate tool-data/all_fasta.loc.sample @ 3:e7ca32457e36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 471c497769f0dbfa92ec1a91f4044062cb5f7a83
| author | iuc | 
|---|---|
| date | Thu, 21 Sep 2017 13:05:25 -0400 | 
| parents | a7fb84abef45 | 
| children | 
| rev | line source | 
|---|---|
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0
 
a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
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1 #This file lists the locations and dbkeys of all the fasta files | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
2 #under the "genome" directory (a directory that contains a directory | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
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 | 
3 #for each build). The script extract_fasta.py will generate the file | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
4 #all_fasta.loc. This file has the format (white space characters are | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
5 #TAB characters): | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
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6 # | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
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7 #<unique_build_id> <dbkey> <display_name> <file_path> | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
8 # | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
9 #So, all_fasta.loc could look something like this: | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
10 # | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
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 | 
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
14 # | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
15 #Your all_fasta.loc file should contain an entry for each individual | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
16 #fasta file. So there will be multiple fasta files for each build, | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
diff
changeset
 | 
17 #such as with hg19 above. | 
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a7fb84abef45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
 
iuc 
parents:  
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 | 
18 # | 
