|
5
|
1 #This is a sample file distributed with Galaxy that enables tools
|
|
|
2 #to use a directory of BWA indexed sequences data files. You will need
|
|
|
3 #to create these data files and then create a bwa_index.loc file
|
|
|
4 #similar to this one (store it in this directory) that points to
|
|
|
5 #the directories in which those files are stored. The bwa_index.loc
|
|
|
6 #file has this format (white space characters are TAB characters):
|
|
|
7 #
|
|
|
8 #<build> <file_base>
|
|
|
9 #
|
|
|
10 #So, for example, if you had phiX indexed stored in
|
|
|
11 #/depot/data2/galaxy/phiX/base/,
|
|
|
12 #then the bwa_index.loc entry would look like this:
|
|
|
13 #
|
|
|
14 #phiX /depot/data2/galaxy/phiX/base/phiX.fa
|
|
|
15 #
|
|
|
16 #and your /depot/data2/galaxy/phiX/base/ directory
|
|
|
17 #would contain phiX.fa.* files:
|
|
|
18 #
|
|
|
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
|
|
|
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
|
|
|
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
|
|
|
22 #...etc...
|
|
|
23 #
|
|
|
24 #Your bwa_index.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 #phiX /depot/data2/galaxy/phiX/base/phiX.fa
|
|
|
29 #hg18 /depot/data2/galaxy/hg18/base/hg18.fa
|
|
|
30 Oryza sativa(IRGSPbuild5) /disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build5.fa
|
|
|
31 Oryza sativa(IRGSPbuild1.0) /disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build1.0.fa
|
|
|
32 Arabidopsis thaliana(TAIR10) /disk/reference/ddbj/distribution_of_polymorphism/TAIR10.fa
|
|
|
33 Zea mays B73(RefGen_v2) /disk/reference/ddbj/distribution_of_polymorphism/ZmB73.RefGen2.fa
|
|
|
34 Sorghum bicolor(phytozome_v9.0_Sbicolor_v1.4) /disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi1.4.fa
|
|
|
35 Sorghum bicolor(phytozome_v9.0_Sbicolor_v2.1) /disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi12.1.fa
|
