diff --git a/script/network_portal.sh b/script/network_portal.sh index 5c2dd9f..cdd31ec 100755 --- a/script/network_portal.sh +++ b/script/network_portal.sh @@ -18,6 +18,7 @@ interactive=$(${cmdprefix}interactive | sed -r '/^\s*$/d') resn=$($SIGNET_ROOT/signet -s --resn | sed -r '/^\s*$/d') sif=$($SIGNET_ROOT/signet -s --sif | sed -r '/^\s*$/d' | xargs readlink -f) forcerm=$($SIGNET_ROOT/signet -s --forcerm | sed -r '/^\s*$/d') +eamil=$($SIGNET_ROOT/signet -s --email | sed -r '/^\s*$/d') function usage() { echo 'Usage:' @@ -41,11 +42,12 @@ function usage() { # echo " --filter To focus on a list of genes" echo " --resn result prefix" echo " --sif singularity container" + echo " --email send notification emails for both two stages if you have mail installed in Linux" exit -1 } [ $? -ne 0 ] && usage -ARGS=`getopt -a -o r: -l net.gexp.data:,net.geno.data:,sig.pair:,net.genepos:,net.genename:,ncis:,r:,cor:,memory:,m:,queue:,q:,walltime:,:w:,nboots:,ncores:,interactive:,resn:,sif:,h:,help -- "$@"` +ARGS=`getopt -a -o r: -l net.gexp.data:,net.geno.data:,sig.pair:,net.genepos:,net.genename:,ncis:,r:,cor:,memory:,m:,queue:,q:,walltime:,:w:,nboots:,ncores:,interactive:,resn:,sif:,email:,h:,help -- "$@"` eval set -- "${ARGS}" @@ -122,6 +124,9 @@ case "$1" in sif=$(readlink -f $sif) $SIGNET_ROOT/signet -s --sif $sif shift;; + --email) + email=$2 + $SIGNET_ROOT/signet -s --email $email --h|--help) usage exit @@ -153,7 +158,7 @@ if [[ "$resn" == *"doesn't exist"* ]]; then exit -1 fi -var="net_gexp net_geno sig_pair net_genename net_genepos cor ncis ncores memory nboots queue walltime interactive resn sif" +var="net_gexp net_geno sig_pair net_genename net_genepos cor ncis ncores memory nboots queue walltime interactive resn sif email" for i in $var do export "${i}"