### executables
JAVA=@JAVA@
PERL=@PERL@
R=@R_EXE@
        

### scripts path
RVboost_scripts=@INSTALL_DIR@/src/

### tools
GATK=@INSTALL_DIR@/bin/gatk/
BEDTOOLS=@INSTALL_DIR@/bin/bedtools/bin/
SAMTOOLS=@INSTALL_DIR@/bin/samtools/
BLAT=@BLAT@
SNPEFF=@INSTALL_DIR@/bin/snpeff/

### references
REF_GENOME=@REF_GENEOME@
HAPMAP=@INSTALL_DIR@/resources/hapmap.ids.txt.gz
REF_FLAT=@INSTALL_DIR@/resources/refFlat.txt
GENEBED=@INSTALL_DIR@/resources/exons.bed
CODING=@INSTALL_DIR@/resources/coding.bed
RNAEDITTING=@INSTALL_DIR@/resources/RNAedit.vcf.gz

####lib
Rlib=@INSTALL_DIR@/Rlibs/

### tool parameters
UnifiedGenotyper_params=-stand_call_conf 0 -stand_emit_conf 0 -dt NONE
