SMALT_VERSION="0.7.6"
BWA_VERSION="0.7.17"
TABIX_VERSION="master"
SAMTOOLS_VERSION="1.3"

smalt_dir=$(pwd)/"smalt-${SMALT_VERSION}-bin"
bwa_dir=$(pwd)/"bwa-${BWA_VERSION}"
tabix_dir=$(pwd)/"tabix-$TABIX_VERSION"
samtools_dir=$(pwd)/"samtools-$SAMTOOLS_VERSION"

update_path () {
  new_dir=$1
  if [[ ! "$PATH" =~ (^|:)"${new_dir}"(:|$) ]]; then
    export PATH=${new_dir}:${PATH}
  fi
}

update_path ${smalt_dir}
update_path ${bwa_dir}
update_path "${tabix_dir}"
update_path "${samtools_dir}"