Mercurial > repos > nate > data_manager_bwa_mem2_index_builder
annotate tool-data/bwa_mem2_index.loc.sample @ 0:c16f7946364b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
| author | nate |
|---|---|
| date | Tue, 29 Jul 2025 17:15:35 +0000 |
| parents | |
| children |
| rev | line source |
|---|---|
|
0
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
2 #to use a directory of BWA indexed sequences data files. You will need |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
3 #to create these data files and then create a bwa_index.loc file |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
4 #similar to this one (store it in this directory) that points to |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
5 #the directories in which those files are stored. The bwa_index.loc |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
6 #file has this format (longer white space characters are TAB characters): |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
7 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
8 #<unique_build_id> <dbkey> <display_name> <file_path> |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
9 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
10 #So, for example, if you had phiX indexed stored in |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
11 #/depot/data2/galaxy/phiX/base/, |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
12 #then the bwa_index.loc entry would look like this: |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
13 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
14 #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
15 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
16 #and your /depot/data2/galaxy/phiX/base/ directory |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
17 #would contain phiX.fa.* files: |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
18 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
22 #...etc... |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
23 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
24 #Your bwa_index.loc file should include an entry per line for each |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
25 #index set you have stored. The "file" in the path does not actually |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
26 #exist, but it is the prefix for the actual index files. For example: |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
27 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
28 #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
29 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
30 #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
31 #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
32 #...etc... |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
33 # |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
34 #Note that for backwards compatibility with workflows, the unique ID of |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
35 #an entry must be the path that was in the original loc file, because that |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
36 #is the value stored in the workflow for that parameter. That is why the |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
37 #hg19 entry above looks odd. New genomes can be better-looking. |
|
c16f7946364b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
diff
changeset
|
38 # |