#This is a sample file distributed with Galaxy that enables tools
#to use a directory of Ariba data files.
#The Arriba script download_references.sh retrieves a genome assembly fasta
#and a related GTF annotation file, then builds a STAR index.
#You will need to create these data files and then create a
#arriba_indexes.loc similar to this one (store it in this
#directory) that points to the directories in which those files are stored.
#The arriba_indexes.loc file has this format (longer white space
#characters are TAB characters):
#
#<unique_build_id>   <display_name>   <genome_fasta_path>	<genome_gtf_path>	<STAR_index_path>
#
#Note that STAR indices can become quite large. 
#
#<unique_build_id>	<display_name>	<genome_fasta_path>	<genome_gtf_path>	<STAR_index_path>
#GRCh38+ENSEMBL93	GRCh38+ENSEMBL93	/depot/GRCh38+ENSEMBL93/genome.fa	/depot/GRCh38+ENSEMBL93/genome.gtf	/depot/GRCh38+ENSEMBL93/STAR_index/
GRCh38+ENSEMBL93	GRCh38+ENSEMBL93	${__HERE__}/test-cache/genome.fasta	${__HERE__}/test-cache/genome.gtf	${__HERE__}/test-cache/STAR_index/