Add choice of run or exec wrapper behaviours

docker/irods_clients/ubuntu/Dockerfile

@@ -143,6 +143,7 @@ COPY --from=installer /usr/local /usr/local
 COPY --from=singularity ./scripts/* /usr/local/bin/
 COPY --from=installer /opt/docker/irods_clients/manifest.json /usr/local/irods_clients/etc/manifest.json
 COPY --from=installer /opt/docker/irods_clients/scripts/docker-entrypoint.sh /usr/local/irods_clients/bin/docker-entrypoint.sh
+COPY --from=installer /opt/docker/irods_clients/scripts/singularity-* /usr/local/bin/
 
 # Configure the singularity-wrapper script
 ENV MANIFEST_PATH="/usr/local/irods_clients/etc/manifest.json"

singularity/scripts/singularity-exec-docker

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -euo pipefail
+
+DOCKER_REGISTRY=${DOCKER_REGISTRY:?required, but not set}
+DOCKER_USER=${DOCKER_USER:?required, but not set}
+DOCKER_IMAGE=${DOCKER_IMAGE:?required, but was not set}
+DOCKER_TAG=${DOCKER_TAG:?required, but not set}
+
+singularity exec "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$@"

singularity/scripts/singularity-run-docker

@@ -1,22 +1,10 @@
 #!/bin/bash
-#
-# Running this script will start an instance of the container, if one is not 
-# already running, and then execute the command in the instance.
-#
-# Cleaning up unwanted instances afterwards is outside the scope of this script.
+
 set -euo pipefail
 
 DOCKER_REGISTRY=${DOCKER_REGISTRY:?required, but not set}
 DOCKER_USER=${DOCKER_USER:?required, but not set}
 DOCKER_IMAGE=${DOCKER_IMAGE:?required, but was not set}
 DOCKER_TAG=${DOCKER_TAG:?required, but not set}
 
-# Colons and slashes are not allowed in Singularity instance names
-instance="$DOCKER_REGISTRY--$DOCKER_USER--$DOCKER_IMAGE--$DOCKER_TAG"
-
-if ! singularity instance list | grep "$instance" 2>&1 >/dev/null ; then
-    singularity instance start \
-        "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$instance" 2>&1 >/dev/null
-fi
-
-singularity exec "instance://$instance" "$@"
+singularity run "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$@"

singularity/scripts/singularity-service-docker

@@ -0,0 +1,22 @@
+#!/bin/bash
+#
+# Running this script will start an instance of the container, if one is not 
+# already running, and then execute the command in the instance.
+#
+# Cleaning up unwanted instances afterwards is outside the scope of this script.
+set -euo pipefail
+
+DOCKER_REGISTRY=${DOCKER_REGISTRY:?required, but not set}
+DOCKER_USER=${DOCKER_USER:?required, but not set}
+DOCKER_IMAGE=${DOCKER_IMAGE:?required, but was not set}
+DOCKER_TAG=${DOCKER_TAG:?required, but not set}
+
+# Colons and slashes are not allowed in Singularity instance names
+instance="$DOCKER_REGISTRY--$DOCKER_USER--$DOCKER_IMAGE--$DOCKER_TAG"
+
+if ! singularity instance list | grep "$instance" 2>&1 | logger -p user.notice -t singularity-service-docker ; then
+    singularity instance start \
+        "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$instance" 2>&1 | logger -p user.notice -t singularity-service-docker
+fi
+
+singularity exec "instance://$instance" "$@"

singularity/scripts/singularity-wrapper

@@ -24,10 +24,22 @@ usage() {
 Install singularity proxy wrappers for the executables listed in a
 container's manifest to a nominated directory.
 
-Usage: $0 [-h] [-i <Docker image name>]
+Two different types of wrapper are available which differ in how
+they run singularity. The default type uses "singularity run",
+while the alternative type uses "singularity exec".
+
+If the "exec" type is used, the wrapper can additionally be made
+to create a long-running service instance on first use and
+subsequently "exec" within that instance. 
+
+Usage: $0
+    [-e]
+    [-h]
+    [-i <Docker image name>]
     [-m <JSON manifest path>]
     [-p <wrapper install prefix>]
     [-r <Docker registry name>]
+    [-s]
     [-t <Docker image tag>]
     [-u <Docker user name>] [-v] <operation>
 
@@ -40,6 +52,8 @@ Operation may be one of:
 Options:
 
  -h  Print usage and exit.
+ -e  Use "singularity exec", rather than "singularity run" in the
+     generated wrappers.
  -i  Docker image name. Required, defaults to the value of the
      environment variable "\$DOCKER_IMAGE" ("$DOCKER_IMAGE").
  -m  Manifest file path. Optional, defaults to the value of the
@@ -48,6 +62,7 @@ Options:
      environment variable \$PREFIX ("$PREFIX").
  -r  Docker registry name. Optional, defaults to the value of the 
      environment variable \$DOCKER_REGISTRY ("$DOCKER_REGISTRY").
+ -s  Start a long-running service instance (implies use of exec).
  -t  Docker image tag. Optional, defaults to the value of the
      environment variable \$DOCKER_TAG ("$DOCKER_TAG").
  -u  Docker user name. Optional, defaults to the value of the
@@ -86,7 +101,7 @@ export DOCKER_TAG="$DOCKER_TAG"
 # time, be permanently set in the installed wrapper. E.g. a candidate
 # is SINGULARITY_CACHEDIR.
 
-"\$(dirname "\${BASH_SOURCE[0]}")/singularity-run-docker" "$exe" "\$@"
+"\$(dirname "\${BASH_SOURCE[0]}")/$singularity_wrap_impl" "$exe" "\$@"
 EOF
 
 chmod +x "$dir/$exe"
@@ -96,7 +111,7 @@ chmod +x "$dir/$exe"
 install_wrappers() {
     local dir="$PREFIX/bin"
     install -d "$dir"
-    cp /usr/local/bin/singularity-run-docker "$PREFIX/bin"
+    cp "/usr/local/bin/$singularity_wrap_impl" "$PREFIX/bin"
 
     for exe in "${wrappers[@]}" ; do
         write_wrapper "$dir" "$exe"
@@ -111,8 +126,13 @@ DOCKER_TAG=${DOCKER_TAG:-latest}
 PREFIX=${PREFIX:-/opt/wtsi-npg}
 MANIFEST_PATH=${MANIFEST_PATH:-"$PREFIX/etc/manifest.json"}
 
-while getopts "hi:m:p:r:t:u:v" option; do
+singularity_wrap_impl="singularity-run-docker"
+
+while getopts "hei:m:p:r:st:u:v" option; do
     case "$option" in
+        e)
+            singularity_wrap_impl="singularity-exec-docker"
+            ;;
         h)
             usage
             exit 0
@@ -129,6 +149,9 @@ while getopts "hi:m:p:r:t:u:v" option; do
         r)
             DOCKER_REGISTRY="$OPTARG"
             ;;
+        s)
+            singularity_wrap_impl="singularity-service-docker"
+            ;;
         t)
             DOCKER_TAG="$OPTARG"
             ;;
@@ -156,14 +179,14 @@ fi
 
 wrappers=($(jq -j '.executable[] + " "' "$MANIFEST_PATH"))
 
-OPERATION="$@"
-if [ -z "$OPERATION" ] ; then
+operation="$@"
+if [ -z "$operation" ] ; then
     usage
     echo -e "\nERROR:\n  An operation argument is required"
     exit 4
 fi
 
-case "$OPERATION" in
+case "$operation" in
     list)
         print_manifest
         exit 0
@@ -173,7 +196,7 @@ case "$OPERATION" in
         ;;
     *)
         usage
-        echo -e "\nERROR:\n  Invalid wrapper operation '$OPERATION'"
+        echo -e "\nERROR:\n  Invalid wrapper operation '$operation'"
         exit 4
         ;;
 esac