#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 fasta_indexes.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The fasta_indexes.loc #file has this format (white space characters are TAB characters): # # # #So, for example, if you had hg19 Canonical indexed stored in # # /depot/data2/galaxy/hg19/sam/, # #then the fasta_indexes.loc entry would look like this: # #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa # #and your /depot/data2/galaxy/hg19/sam/ directory #would contain hg19canon.fa and hg19canon.fa.fai files. # #Your fasta_indexes.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: # #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa