Mercurial > repos > ryanmorin > nextgen_variant_identification
view sam_fa_indices.loc.sample @ 3:d0c27980d703
Deleted selected files
author | ryanmorin |
---|---|
date | Wed, 12 Oct 2011 19:55:06 -0400 |
parents | f7c0e4d94423 |
children |
line wrap: on
line source
#This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a sam_fa_indices.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The sam_fa_indices.loc #file has this format (white space characters are TAB characters): # #index <seq> <location> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/sam/, #then the sam_fa_indices.loc entry would look like this: # #index hg18 /depot/data2/galaxy/sam/hg18.fa # #and your /depot/data2/galaxy/sam/ directory #would contain hg18.fa and hg18.fa.fai files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai # #Your sam_fa_indices.loc file should include an entry per line for #each index set you have stored. The file in the path does actually #exist, but it should never be directly used. Instead, the name serves #as a prefix for the index file. For example: # #index hg18 /depot/data2/galaxy/sam/hg18.fa #index hg19 /depot/data2/galaxy/sam/hg19.fa