|
11
|
1 #This is a sample file distributed with Galaxy that enables tools
|
|
|
2 #to use a directory of Samtools indexed sequences data files. You will need
|
|
|
3 #to create these data files and then create a fasta_indexes.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 fasta_indexes.loc
|
|
|
6 #file has this format (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 hg19 Canonical indexed stored in
|
|
|
11 #
|
|
|
12 # /depot/data2/galaxy/hg19/sam/,
|
|
|
13 #
|
|
|
14 #then the fasta_indexes.loc entry would look like this:
|
|
|
15 #
|
|
|
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
|
|
|
17 #
|
|
|
18 #and your /depot/data2/galaxy/hg19/sam/ directory
|
|
|
19 #would contain hg19canon.fa and hg19canon.fa.fai files.
|
|
|
20 #
|
|
|
21 #Your fasta_indexes.loc file should include an entry per line for
|
|
|
22 #each index set you have stored. The file in the path does actually
|
|
|
23 #exist, but it should never be directly used. Instead, the name serves
|
|
|
24 #as a prefix for the index file. For example:
|
|
|
25 #
|
|
|
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
|
|
|
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
|
|
|
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
|
|
|
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
|
