Mercurial > repos > bgruening > deeptools_multi_bam_summary
annotate tool-data/lastz_seqs.loc.sample @ 13:0f4f3b4ebfa9 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
author | bgruening |
---|---|
date | Fri, 31 Mar 2017 17:52:40 -0400 |
parents | 04b612e24e62 |
children |
rev | line source |
---|---|
0
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
2 #to use a directory of 2bit genome files for use with deepTools. |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
3 #This file is named lastz_seqs.loc file to make use of an already existing loc |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
4 #file from the lastz tool that is created by the twobit data-manager. |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
5 #You will need to supply these files and then create a lastz_seqs.loc file |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
6 #similar to this one (store it in this directory) that points to |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
7 #the directories in which those files are stored. The lastz_seqs.loc |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
8 #file has this format: |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
9 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
10 #<unique_build_id> <display_name> <file_path> |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
11 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
12 #So, for example, if your lastz_seqs.loc began like this: |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
13 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
14 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
15 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
16 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
17 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
18 #then your /depot/data2/galaxy/twobit/ directory |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
19 #would need to contain the following 2bit files: |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
20 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
21 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
22 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
23 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
24 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
25 #Your lastz_seqs.loc file should include an entry per line for |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
26 #each file you have stored that you want to be available. Note that |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
27 #your files should all have the extension '2bit'. |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
28 # |
04b612e24e62
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
bgruening
parents:
diff
changeset
|
29 #Please note that the <unique_build_id> is also used as "Species name abbreviation". |