Mercurial > repos > iuc > jbrowse
annotate tool-data/all_fasta.loc.sample @ 42:6cd09d7b5f37 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
author | iuc |
---|---|
date | Sat, 06 Feb 2021 12:01:13 +0000 |
parents | f422ba2e9aa5 |
children |
rev | line source |
---|---|
9
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
1 #This file lists the locations and dbkeys of all the fasta files |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
2 #under the "genome" directory (a directory that contains a directory |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
3 #for each build). The script extract_fasta.py will generate the file |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
4 #all_fasta.loc. This file has the format (white space characters are |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
5 #TAB characters): |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
6 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
7 #<unique_build_id> <dbkey> <display_name> <file_path> |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
8 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
9 #So, all_fasta.loc could look something like this: |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
10 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
14 # |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
15 #Your all_fasta.loc file should contain an entry for each individual |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
16 #fasta file. So there will be multiple fasta files for each build, |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
17 #such as with hg19 above. |
f422ba2e9aa5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba
iuc
parents:
diff
changeset
|
18 # |