|
5
|
1 # bowtie2_indices.loc.sample
|
|
|
2 # This is a *.loc.sample file distributed with Galaxy that enables tools
|
|
|
3 # to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
|
|
|
4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
|
|
|
5 # First create these data files and save them in your own data directory structure.
|
|
|
6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
|
|
|
7 # Copy this file, save it with the same name (minus the .sample),
|
|
|
8 # follow the format examples, and store the result in this directory.
|
|
|
9 # The file should include an one line entry for each index set.
|
|
|
10 # The path points to the "basename" for the set, not a specific file.
|
|
|
11 # It has four text columns seperated by TABS.
|
|
|
12 #
|
|
|
13 # <unique_build_id> <dbkey> <display_name> <file_base_path>
|
|
|
14 #
|
|
|
15 # So, for example, if you had hg18 indexes stored in:
|
|
|
16 #
|
|
|
17 # /depot/data2/galaxy/hg19/bowtie2/
|
|
|
18 #
|
|
|
19 # containing hg19 genome and hg19.*.bt2 files, such as:
|
|
|
20 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
|
|
|
21 # -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
|
|
|
22 # -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
|
|
|
23 # -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
|
|
|
24 # -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
|
|
|
25 # -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
|
|
|
26 # -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
|
|
|
27 #
|
|
|
28 # then the bowtie2_indices.loc entry could look like this:
|
|
|
29 #
|
|
|
30 #
|
|
|
31 hg38 Homo sapiens - GRCh38 hsa.gff3 Homo sapiens
|
|
|
32 mm10 Mus musculus - GRCm38 mmu.gff3 Mus musculus
|
|
|
33 BosTau5 Bos taurus - Btau_5.0.1 bta.gff3 Bos taurus
|
|
|
34 Arabidopsis_thaliana_TAIR10 Arabidopsis thaliana - TAIR10 ath.gff3 Arabidopsis thaliana
|
|
|
35 droSim1 Drosophila simulans - dsim_caf1 dsi.gff3 Drosophila simulans
|
|
|
36 #
|
|
|
37 #
|
|
|
38 #
|
|
|
39 #
|
