paths

##This file will provide LTR_retriever paths to dependent programs.
##You can leave the respective paths empty if programs are accessible through ENV (i.e. exported to .bashrc)
##If you specify a path, please make sure that the required program(s) is directly contained in that path but not in any child directories.
##e.g. BLAST+=/opt/software/BLAST+/2.2.30--GCC-4.4.5/bin/
##LTR_retriever is build based on GenomeTools/1.5.4, BLAST+/2.2.28, BLAST/2.2.26, CDHIT/4.6.1c, HMMER/3.1b2, RepeatMasker/4.0.0, Tandem Repeats Finder 4.07b, and TEsorter 1.3

BLAST+= 	#a path that contains makeblastdb, blastn, blastx
RepeatMasker=	#a path that contains RepeatMasker
HMMER=		#a path that contains hmmsearch
CDHIT=		#a path that contains cd-hit-est (preferred). CDHIT and BLAST are replaceable
BLAST=		#a path that contains blastclust (optional)
TEsorter=	#a path that contains TEsorter