diff --git a/wGRR b/wGRR index d1b847eac462b38e8dd7c0bfa94e198ad0c1d3b0..bdcdaf71f325b94750ef404e7736ff667c0d17fe 100755 --- a/wGRR +++ b/wGRR @@ -5,16 +5,13 @@ trap 'rm -rf "$tmp"' EXIT export LC_ALL=C - SECONDS=0 - readonly VERSION=0.4 - bold=$(tput bold) normal=$(tput sgr0) display_usage() { - echo "$(echo ${ZSH_ARGZERO} | awk 'BEGIN{FS="/"}{print $NF}') version ${VERSION}" + echo "wGRR version ${VERSION}" echo "${bold}USAGE:${normal} $ZSH_ARGZERO -f <fasta_file> [OPTIONS]" echo "" echo "${bold}MANDATORY PARAMETERS:${normal}" @@ -56,7 +53,7 @@ fi # print version if [ "$1" = "-v" ] || [ "$1" = "--version" ]; then - echo "$(echo ${ZSH_ARGZERO} | awk 'BEGIN{FS="/"}{print $NF}') version ${VERSION}"; + echo "wGRR version ${VERSION}"; exit 0; fi @@ -147,26 +144,18 @@ if [[ $OUT == "N.O.O.U.T" ]] ; then OUT=$(basename $tmp) fi -echo "[INFO] -- $(echo ${ZSH_ARGZERO} | awk 'BEGIN{FS="/"}{print $NF}') version ${VERSION}" -echo "[INFO] -- The command is:" -echo "[INFO] -- $ZSH_ARGZERO $@" - -################################# -########### TO DO ############### -################################# -## Check dependencies -if [[ ! -f wGRR.awk ]] ; then - echo "[ERROR] -- awk script wGRR.awk not found." - exit 1 -fi - ## Get partition (if sbatch) or check nproc (if local/Check number of threads if [[ $SLURM_JOBID != "" ]] ; then PARTITION=$(squeue -j $SLURM_JOBID -o "%P" -h) BATCHFLAG=$(squeue -j $SLURM_JOBID --Format=batchflag -h | awk '{print $1}') fi +echo "[INFO] -- wGRR version ${VERSION}" + if [[ $BATCHFLAG == 0 ]] ; then + echo "[INFO] -- The command is:" + echo "[INFO] -- ./wGRR $@" + if [[ $THREADS -gt $(nproc) ]] ; then echo "[ERROR] -- You required $THREADS threads but your machine has $(nproc) cores." exit 1 @@ -176,6 +165,8 @@ if [[ $BATCHFLAG == 0 ]] ; then module load openmpi fi else + echo "[INFO] -- The command is:" + echo "[INFO] -- $(scontrol show job ${SLURM_JOBID} | awk '/ +Command/{n=split($0,a,"=");print a[n]}')" if [[ ! -f wGRR_mem.awk ]] ; then if [[ $ARRAYSIZE > 10000 ]] ; then echo "[ERROR] -- awk script wGRR_mem.awk not found." @@ -184,6 +175,16 @@ else fi fi +if [[ ! -f wGRR.awk ]] ; then + echo "[ERROR] -- awk script wGRR.awk not found." + exit 1 +fi + +if [[ ! -f wGRR_worker.zsh ]] ; then + echo "[ERROR] -- awk script wGRR_worker.zsh not found." + exit 1 +fi + ## Check awk if ! AWKEXE=$(command -v gawk) ; then if ! AWKEXE=$(command -v awk) ; then