From 7689c82dc35b9b11b6543a12dc893afdc49d4eb2 Mon Sep 17 00:00:00 2001
From: Julien Guglielmini <julien.guglielmini@pasteur.fr>
Date: Thu, 17 Feb 2022 16:18:38 +0100
Subject: [PATCH] Better log
---
wGRR | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)
diff --git a/wGRR b/wGRR
index d1b847e..bdcdaf7 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
--
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