view gatk2_sorted_picard_index.loc.sample @ 33:76f8ca47b810 draft

Omit --read_filter param included by default

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Picard dict and associated files. You will need
#to create these data files and then create a picard_index.loc file 
#similar to this one (store it in this directory) that points to 
#the directories in which those files are stored. The picard_index.loc 
#file has this format (longer white space is the TAB character):
#
#<unique_build_id>	<dbkey>		<display_name>		<fasta_file_path>
#
#So, for example, if you had hg18 indexed and stored in 
#/depot/data2/galaxy/srma/hg18/,
#then the srma_index.loc entry would look like this:
#
#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
#
#and your /depot/data2/galaxy/srma/hg18/ directory
#would contain the following three files:
#hg18.fa
#hg18.dict
#hg18.fa.fai
#
#The dictionary file for each reference (ex. hg18.dict) must be 
#created via Picard (http://picard.sourceforge.net). Note that
#the dict file does not have the .fa extension although the
#path list in the loc file does include it.
#
hg18	hg18	hg18	/data/galaxy/ext-tool-data/picard/hg18.fa
hg19	hg19	hg19	/data/galaxy/ext-tool-data/picard/hg19.fa
mm8	mm8	mm8	/data/galaxy/ext-tool-data/picard/mm8.fa
mm9	mm9	mm9	/data/galaxy/ext-tool-data/picard/mm9.fa