diff --git a/bin/HiC-Pro b/bin/HiC-Pro index 887ce1b..9189c04 100755 --- a/bin/HiC-Pro +++ b/bin/HiC-Pro @@ -127,6 +127,15 @@ if [[ -z $INPUT || -z $OUTPUT || -z $CONF ]]; then fi +## check if ice is in the PATH +if [[ $MAKE_OPTS == "" || $MAKE_OPTS =~ "ice_norm" ]]; then + which ice > /dev/null + if [ $? != "0" ]; then + echo -e "Error: The 'ice' command is not in your path. Please check where the 'iced' python package has been installed and update your PATH !" + exit 1; + fi +fi + ##################### ## Check Config file ##################### @@ -181,14 +190,6 @@ if [[ ! -z $ALLELE_SPECIFIC_SNP && ! -r $ALLELE_SPECIFIC_SNP ]]; then die "ALLELE_SPECIFIC_SNP $ALLELE_SPECIFIC_SNP not found. Exit" fi -## check if ice is in the PATH -if [[ $MAKE_OPTS =~ "ice_norm" ]]; then - which ice > /dev/null; - if [ $? != "0" ]; then - echo -e "The 'ice' command is not in your path. Please check where the 'iced' python package has been installed and update your PATH !" - exit 1; - fi -fi ##################### ## Check step option #####################