Mercurial > repos > iuc > data_manager_bowtie_index_builder
annotate tool-data/bowtie_indices.loc.sample @ 3:ea5faedd0795 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 18:06:27 -0400 |
| parents | 0a0c648498e2 |
| children |
| rev | line source |
|---|---|
|
0
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
1 #This is a sample file distributed with Galaxy that enables tools |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
2 #to use a directory of Bowtie indexed sequences data files. You will |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
3 #need to create these data files and then create a bowtie_indices.loc |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
4 #file similar to this one (store it in this directory) that points to |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
5 #the directories in which those files are stored. The bowtie_indices.loc |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
6 #file has this format (longer white space characters are TAB characters): |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
7 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
8 #<unique_build_id> <dbkey> <display_name> <file_base_path> |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
9 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
10 #So, for example, if you had hg18 indexed stored in |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
11 #/depot/data2/galaxy/bowtie/hg18/, |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
12 #then the bowtie_indices.loc entry would look like this: |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
13 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
15 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
16 #and your /depot/data2/galaxy/bowtie/hg18/ directory |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
17 #would contain hg18.*.ebwt files: |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
18 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
22 #...etc... |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
23 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
24 #Your bowtie_indices.loc file should include an entry per line for each |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
25 #index set you have stored. The "file" in the path does not actually |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
26 #exist, but it is the prefix for the actual index files. For example: |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
27 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
31 #...etc... |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
32 # |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
33 #Note that for backwards compatibility with workflows, the unique ID of |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
34 #an entry must be the path that was in the original loc file, because that |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
35 #is the value stored in the workflow for that parameter. That is why the |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
36 #hg19 entry above looks odd. New genomes can be better-looking. |
|
0a0c648498e2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
iuc
parents:
diff
changeset
|
37 # |