4
|
1 #This is a sample file distributed with Galaxy that enables the DC_Genotyper
|
|
2 #tool to locate genome files for use with twoBitToFa, and IGVtools. You will
|
|
3 #need to supply these files and then create a DC_Genotyper.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 DC_Genotyper.loc
|
|
6 #file has this format (white space characters are TAB characters):
|
|
7 #
|
10
|
8 #<unique_build_id> <dbkey> <display_name> <2bit_path,IGVtools_genome.path>
|
4
|
9 #
|
|
10 #for example:
|
|
11 #
|
10
|
12 #hg19 hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit,/depot/data2/galaxy/igvtools/hg19.chrom.sizes
|
4
|
13 #
|
|
14 #then your /depot/data2/galaxy/twobit/ directory
|
|
15 #would need to contain the following 2bit files:
|
|
16 #
|
|
17 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
|
|
18 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
|
|
19 #
|
|
20 # your igvtools folder needs the following files:
|
|
21 #
|
|
22 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.chrom.sizes
|
|
23 #
|
|
24 # igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored.
|
|
25 # example genome files are included in the installation location of the package_igvtools repository.
|
|
26
|