Mercurial > repos > devteam > bwa
annotate tool-data/bwa_mem_index.loc.sample @ 14:8a98cfb7ea55 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
author | iuc |
---|---|
date | Wed, 05 May 2021 18:21:27 +0000 |
parents | c9c78719ef26 |
children |
rev | line source |
---|---|
0
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
2 #to use a directory of BWA indexed sequences data files. You will need |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
3 #to create these data files and then create a bwa_index.loc file |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
4 #similar to this one (store it in this directory) that points to |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
5 #the directories in which those files are stored. The bwa_index.loc |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
6 #file has this format (longer white space characters are TAB characters): |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
7 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
8 #<unique_build_id> <dbkey> <display_name> <file_path> |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
9 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
10 #So, for example, if you had phiX indexed stored in |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
11 #/depot/data2/galaxy/phiX/base/, |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
12 #then the bwa_index.loc entry would look like this: |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
13 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
15 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
16 #and your /depot/data2/galaxy/phiX/base/ directory |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
17 #would contain phiX.fa.* files: |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
18 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
22 #...etc... |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
23 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
24 #Your bwa_index.loc file should include an entry per line for each |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
25 #index set you have stored. The "file" in the path does not actually |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
26 #exist, but it is the prefix for the actual index files. For example: |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
27 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
32 #...etc... |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
33 # |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
34 #Note that for backwards compatibility with workflows, the unique ID of |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
35 #an entry must be the path that was in the original loc file, because that |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
36 #is the value stored in the workflow for that parameter. That is why the |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
37 #hg19 entry above looks odd. New genomes can be better-looking. |
c9c78719ef26
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff
changeset
|
38 # |