prepare new release

singularity/test_container.sh

@@ -1,46 +1,135 @@
 #!/usr/bin/env bash
 
-# Config for Slurm
+# Test script for BeeDeeM singularity container
+# How to?
+# Step 1: build image with: singularity build -f beedeem-4.7.4.sif Singularity
+#         (update version to match BDM_VERSION variable, below)
+# Step 2: test with either
+#         a. ./test_container.sh
+#         b. qsub test_container.sh (PBS Pro)
+#         c. srun test_container.sh (slurm, direct execution)
+#
+# P. Durand (SeBiMER, Ifremer), last update on Nov 2022
+
+# Sample config for Slurm; adapt partition to your cluster configuration
 #SBATCH -p fast
 #SBATCH --mem 4GB
 #SBATCH -t 0-02:00                  #(D-HH:MM)
 #SBATCH -o lftp.%N.%j.out           # STDOUT
 #SBATCH -e lftp.%N.%j.err           # STDERR
 
-# Config for PBS pro
+# Sample config for PBS pro; adapt queue to you cluster configuration
 #PBS -q ftp
 #PBS -l walltime=02:00:00
 #PBS -l mem=4g
 #PBS -l ncpus=2
 
+# Version of BeeDeeM to test
+BDM_VERSION=4.7.4
+# Default working directory to test BeeDeeM Singularity image.
+# Il will be overriden below, given host platform
+BDM_SCRATCH_DIR=/tmp
+# What is the name of the BeeDeeM image
+BDM_SING_IMG_NAME=beedeem-${BDM_VERSION}.sif
+# Where to find the BeeDeeM image
+BDM_SING_IMG_HOME=$HOME/devel/BeeDeeM/singularity
+# If BeeDeeM image is not located in above path, try to get it from SeBiMER repo
+BDM_SING_PUBLIC_REPO=https://data-dataref.ifremer.fr/bioinfo/ifremer/sebimer/tools/ORSON
 
-# Test script for BeeDeeM singularity container
-# How to?
-# Step 1: build image with: singularity build -f beedeem-4.7.2.sif Singularity
-#         (update version to match BDM_VERSION variable, below)
-# Step 2: test with: ./test_container.sh
+# --------
+# FUNCTION: figure out whether or not a command exists.
+#  arg1: a command name.
+#  return: 0 if success 
+hasCommand () {
+    command -v "$1" >/dev/null 2>&1
+}
 
+# --------
+# FUNCTION: download a file from a remote server.
+#           URL is downloaded using curl or wget, saved in
+#           current directory and named using provided local
+#           file name. Function is capable of resuming a
+#           previous aborted job.
+#  arg1: local file name
+#  arg2: URL
+#  return: 0 if success
+function downloadFile(){
+  filename=$1
+  url=$2
+  #Use verbose-less download mode to avoid having huge log.
+  #Use curl first, since it's more easy to get only error 
+  #messages if any
+  if hasCommand curl; then
+    CMD="curl -sSL -o $filename -C - $url"
+  elif hasCommand wget; then
+    CMD="wget -c -q $url -O $filename"
+  else
+    echo "ERROR: Could not find curl nor wget, please install one of them."
+    return 1
+  fi
+  echo $CMD
+  eval $CMD && return 0 || return 1
+}
+
+# Depending on host platform, load singularity env
+if hasCommand qstat; then
+  hname=$(hostname)
+  if [[ $hname == *"datarmor"* ]]; then
+    echo "running on DATARMOR using PBS Pro scheduler"
+    source /etc/profile.d/modules.sh
+    module purge
+    module load singularity/3.4.1
+    BDM_SCRATCH_DIR=$SCRATCH
+  fi
+elif hasCommand sbatch; then
+  hname=$(hostname -A)
+  if [[ $hname == *"roscoff"* ]]; then
+    echo "running on ABiMS using SLURM scheduler"
+    BDM_SCRATCH_DIR=$HOME
+  fi
+else
+  echo "Cannot figure out which job scheduler is available."
+  echo "  Execute BeeDeeM directly on THIS computer"
+fi
 
 # Configure BeeDeeM banks and working directories
-SCRATCH="$HOME/test_beedeem"
-BDM_BANKS_DIR=$SCRATCH/banks
-BDM_WORK_DIR=$SCRATCH/working
+BDM_SCRATCH_DIR="$BDM_SCRATCH_DIR/test_beedeem"
+BDM_BANKS_DIR="$BDM_SCRATCH_DIR/banks"
+BDM_WORK_DIR="$BDM_SCRATCH_DIR/working"
+
+# Check existence of the BeeDeeM image
+if [ ! -e "$BDM_SING_IMG_HOME/$BDM_SING_IMG_NAME" ]; then
+  echo "WARN: $BDM_SING_IMG_HOME/$BDM_SING_IMG_NAME not found."
+  echo "      Trying to downlod from: $BDM_SING_PUBLIC_REPO/$BDM_SING_IMG_NAME"
+  cd $BDM_WORK_DIR
+  downloadFile "$BDM_SING_IMG_NAME" "$BDM_SING_PUBLIC_REPO/$BDM_SING_IMG_NAME"
+  RET_CODE=$?
+  cd -
+  BDM_SING_IMG_HOME=$BDM_WORK_DIR
+  if [ ! $RET_CODE -eq 0 ]; then
+     echo "ERROR: unable fo get BeeDeeM image"
+     exit 1
+  fi 
+fi
+
+# Configure Singularity runner
+BDM_BINDS="--bind ${BDM_WORK_DIR} --bind ${BDM_BANKS_DIR}"
+BDM_SINGULITY_IMG="$BDM_SING_IMG_HOME/$BDM_SING_IMG_NAME"
+# For debugging if neeeded: dump all BDM_XXX variables
+( set -o posix ; set ) | grep "BDM_"
+
 #rm -rf $BDM_BANKS_DIR
 mkdir -p $BDM_BANKS_DIR
 #rm -rf $BDM_WORK_DIR
 mkdir -p $BDM_WORK_DIR
 
-# Configure Singularity runner
-BDM_VERSION=4.7.2
-BDM_BINDS="--bind ${BDM_WORK_DIR} --bind ${BDM_BANKS_DIR}"
-BDM_SINGULITY_IMG="beedeem-${BDM_VERSION}.sif"
-
 # Prepare env variables to be used by BeeDeeM inside the container (mandatory)
 export KL_JRE_ARGS="-Xms128M -Xmx2048M -Djava.io.tmpdir=${BDM_WORK_DIR} -DKL_LOG_TYPE=console"
 export KL_WORKING_DIR=${BDM_WORK_DIR}
 export KL_mirror__path=${BDM_BANKS_DIR}
 
 # Set the banks to install
+# These are '.dsc' files located in BeeDeeM image at path /opt/beedeem/conf/descriptors
 DESCRIPTOR="SwissProt_human,PDB_proteins,MEROPS_PepUnits"
 
 # Now, let's start a simple installation
@@ -51,10 +140,12 @@ echo "tail -f $BDM_WORK_DIR/log"
 singularity run \
   ${BDM_BINDS} \
   ${BDM_SINGULITY_IMG} \
-  install.sh -desc ${DESCRIPTOR} >& ${BDM_WORK_DIR}/log
+  install.sh -desc ${DESCRIPTOR} >& ${BDM_WORK_DIR}/log 2>&1
 
-if [ ! $? -eq 0 ]; then
-  echo "FAILED.   Review log file:"
+if [ $? -eq 0 ]; then
+  echo "SUCCESS"
+else
+  echo "FAILED.   Review log file: $BDM_WORK_DIR/log"
   exit 1
 fi