Mercurial > repos > devteam > bowtie_wrappers

annotate tool-data/bowtie_indices.loc.sample @ 5:cc439755faab draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 8e2dbf796d0e7a8a00b7ff70a26c0c4f1a6f8cba
author devteam
date Mon, 15 May 2017 20:57:12 -0400
parents 4926b3e1e2fe
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that enables tools
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
2 #to use a directory of Bowtie indexed sequences data files. You will
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
3 #need to create these data files and then create a bowtie_indices.loc
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 #file similar to this one (store it in this directory) that points to
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 #the directories in which those files are stored. The bowtie_indices.loc
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 #file has this format (longer white space characters are TAB characters):
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
7 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
10 #So, for example, if you had hg18 indexed stored in
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 #/depot/data2/galaxy/bowtie/hg18/,
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 #then the bowtie_indices.loc entry would look like this:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
13 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 #and your /depot/data2/galaxy/bowtie/hg18/ directory
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
17 #would contain hg18.*.ebwt files:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
18 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 #...etc...
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
24 #Your bowtie_indices.loc file should include an entry per line for each
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25 #index set you have stored. The "file" in the path does not actually
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 #exist, but it is the prefix for the actual index files. For example:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
27 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 #...etc...
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 #
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
33 #Note that for backwards compatibility with workflows, the unique ID of
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 #an entry must be the path that was in the original loc file, because that
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
35 #is the value stored in the workflow for that parameter. That is why the
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
36 #hg19 entry above looks odd. New genomes can be better-looking.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
37 #