first commit

rasta_exp/launch-container.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env bash
+
+# DOCKER OR SINGULARITY ?
+MODE=$1
+TOOL_NAME=$2
+CONTAINER_IMG=$3
+WORKDIR=$4
+TMP_DIR=$5
+APK_FILENAME=$6
+
+[[ -z "$MODE" ]] || [[ -z "$TOOL_NAME" ]] || [[ -z "$CONTAINER_IMG" ]] || [[ -z "$WORKDIR" ]] || [[ -z "$TMP_DIR" ]] || [[ -z "$APK_FILENAME" ]] && (echo MISSING parameters; exit 1)
+
+ENV_FILE="./envs/${TOOL_NAME}.env"
+if [[ -e "./envs/${TOOL_NAME}_medium.env"  ]]
+then
+	ENV_FILE=./envs/${TOOL_NAME}_medium.env
+	echo USING medium ENV : $ENV_FILE
+fi
+
+#TODO Handle env files for docker/singularity: param   --env-file=
+if [[ "DOCKER" == "$MODE" ]]; then
+    # DOCKER
+    docker run --read-only -it --env-file=${ENV_FILE} --tmpfs /run --tmpfs /tmp --mount type=bind,source=${WORKDIR},destination=/mnt --user=$(id -u):$(id -g) -t ${CONTAINER_IMG} /run.sh ${TIMEOUT} ${APK_FILENAME}
+fi
+if [[ "SINGULARITY" == "$MODE" ]]; then
+    # SINGULARITY
+    echo ${TMP_WORKDIR}
+    singularity exec --net --network=none --no-home --cleanenv --env-file=${ENV_FILE} --bind ${WORKDIR}:/mnt --bind ${TMP_DIR}:/tmp -c ${CONTAINER_IMG}.sif /run.sh ${TIMEOUT} ${APK_FILENAME}
+fi