Mercurial > repos > bgruening > hicup_digester
comparison tool-data/bowtie2_indices.loc.sample @ 0:a47a96d2721a draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author | bgruening |
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date | Thu, 09 Mar 2017 09:30:54 -0500 |
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1 #This is a sample file distributed with Galaxy that enables tools | |
2 #to use a directory of Bowtie2 indexed sequences data files. You will | |
3 #need to create these data files and then create a bowtie_indices.loc | |
4 #file similar to this one (store it in this directory) that points to | |
5 #the directories in which those files are stored. The bowtie2_indices.loc | |
6 #file has this format (longer white space characters are TAB characters): | |
7 # | |
8 #<unique_build_id> <dbkey> <display_name> <file_base_path> | |
9 # | |
10 #So, for example, if you had hg18 indexed stored in | |
11 #/depot/data2/galaxy/bowtie2/hg18/, | |
12 #then the bowtie2_indices.loc entry would look like this: | |
13 # | |
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 | |
15 # | |
16 #and your /depot/data2/galaxy/bowtie2/hg18/ directory | |
17 #would contain hg18.*.ebwt files: | |
18 # | |
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt | |
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt | |
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt | |
22 #...etc... | |
23 # | |
24 #Your bowtie2_indices.loc file should include an entry per line for each | |
25 #index set you have stored. The "file" in the path does not actually | |
26 #exist, but it is the prefix for the actual index files. For example: | |
27 # | |
28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon | |
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full | |
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 | |
31 #...etc... | |
32 # | |
33 #Note that for backwards compatibility with workflows, the unique ID of | |
34 #an entry must be the path that was in the original loc file, because that | |
35 #is the value stored in the workflow for that parameter. That is why the | |
36 #hg19 entry above looks odd. New genomes can be better-looking. | |
37 # |