configs.cf

#!/bin/sh

AGAPE_DIR=/srv/gs1/projects/cherry/giltae/AGAPE
REF_NAME=yeast
CFG_DIR=$AGAPE_DIR/cfg_files
PROTEIN1=$CFG_DIR/yeast_protein.fasta # reference proteins in FASTA
EST1=$CFG_DIR/yeast_est.fasta # reference EST in FASTA
PROTEIN2=$CFG_DIR/fungi_protein.fasta # larger set of proteins in FASTA 
EST2=$CFG_DIR/fungi_est.fasta # larger set of EST in FASTA
REPEAT_PROTEIN=$CFG_DIR/te_proteins.fasta # larger set of EST in FASTA

REF_DIR=$AGAPE_DIR/reference
REF_FASTA=$REF_DIR/$REF_NAME.fasta
REF_GFF=$REF_DIR/$REF_NAME.gff

ABYSS=/srv/gs1/projects/cherry/apps/abyss/bin
SGA=$AGAPE_DIR/programs/SGA/bin
SGA_src=$AGAPE_DIR/programs/SGA/sga-master/src/bin
BLAST=$AGAPE_DIR/programs/BLAST/bin
axtChainNet=$AGAPE_DIR/programs/axtChainNet
AUGUSTUS=$AGAPE_DIR/programs/augustus/augustus.2.5/bin
AUGUSTUS_REF=saccharomyces # check SPECIES.list
MAKER=/srv/gs1/projects/cherry/apps/maker/bin
SNAP=/srv/gs1/projects/cherry/apps/SNAP/snap
GeneMark=/srv/gs1/projects/cherry/apps/GeneMark_S/genemark_suite_linux_64/gmsuite/gmsn.pl
genemark_mod=/srv/gs1/projects/cherry/giltae/strains/GeneMark_model/GeneMark_hmm.mod 
BWA=/srv/gs1/projects/cherry/apps/bwa-0.6.2
SAMTOOLS=/srv/gs1/projects/cherry/apps/samtools-0.1.18
BEDTOOLS=/srv/gs1/projects/cherry/apps/BEDTools/BEDTools-Version-2.16.2/bin

BIN=$AGAPE_DIR/bin