annotate tool-data/all_fasta.loc.sample @ 3:dee617b27094 draft default tip

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 44e872b808f88eacd05963fc2478da2c07b50228
author wolma
date Thu, 22 Mar 2018 10:31:44 -0400
parents d801b0675eb5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
5 #TAB characters):
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
6 #
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
8 #
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
10 #
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
14 #
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
17 #such as with hg19 above.
d801b0675eb5 planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
wolma
parents:
diff changeset
18 #