Mercurial > repos > iuc > jbrowse

annotate all_fasta.loc.sample @ 32:6b774e9d6387 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/jbrowse commit df0ef2f7aaf34e585edbf88654fec9dd9e6acff1
author iuc
date Tue, 16 Jul 2019 05:08:10 -0400
parents 1e74f16adaa1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
5 #TAB characters):
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
6 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
8 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
10 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
14 #
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
17 #such as with hg19 above.
1e74f16adaa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
iuc
parents:
diff changeset
18 #