Mercurial > repos > iuc > snippy

annotate tool-data/all_fasta.loc.sample @ 12:fa016f1eea1a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 7dec701af24e00b3328459f0a823eefd461237bb"
author iuc
date Wed, 07 Apr 2021 11:24:48 +0000
parents 0aa87d97847f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
5 #TAB characters):
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
6 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
8 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
10 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
14 #
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
17 #such as with hg19 above.
0aa87d97847f "planemo upload commit 13d17dd18915767d3ca5bbd92ce3e5e80a287112"
iuc
parents:
diff changeset
18 #