Checking integrity of moved gz files (generate a bsub)

check_mk_bsub.sh

+#!/bin/bash
+
+MAIN_SCRIPTS=~itopols2/genomics
+ORIGDIR='/data2/unige/fig/UHTS/GAII'
+
+. $MAIN_SCRIPTS/rta_api.sh
+
+
+QUEUE=long
+
+declare -a DIRS
+DIRS=( $(find -P "${ORIGDIR}/" -maxdepth 1 -type d -regextype posix-extended -regex "(.*/)?${RUNRX}" -printf '%f\n' | sort -r) )
+
+cat << BSUB_END
+#!/bin/bash
+
+#BSUB -L /bin/bash
+#BSUB -R "span[hosts=1]"
+#BSUB -R "rusage[mem=256]"
+#BSUB -M 262144
+#BSUB -n 1
+#BSUB -q ${QUEUE}
+#BSUB -J "checkdirs[1-${#DIRS[@]}]"
+#BSUB -u bioinfogenomics@unige.ch
+#BSUB -N
+#BSUB -W 100:59
+
+DIRS=( '' ${DIRS[@]} )
+
+DIR="\${DIRS[\$LSB_JOBINDEX]}"
+
+# check if dir name is ok
+if [ -z "\${DIR}" ]; then
+	echo "wrong job index \$LSB_JOBINDEX"
+	exit 1;
+fi
+if [ ! -d "${BASEDIR}/\${DIR}" ]; then
+	echo "${BASEDIR}/\${DIR} : bad directory"
+	exit 1;
+fi
+
+# test and report errors
+ERROR=0
+for Z in \$(find "${BASEDIR}/\${DIR}" -type f -name '*.gz'); do
+	if gunzip --test "\${Z}"; then
+		:
+	else
+		echo "\${Z} : error"
+		(( ERROR++ ))
+	fi
+done
+if (( ERROR > 0 )); then
+	echo "There were errors in ${BASEDIR}/\${DIR}"
+	exit 1;
+else
+	echo "${BASEDIR}/\${DIR} : Everything okay !"
+	exit 0;
+fi
+
+
+BSUB_END