ENH Add docker_wrap script mentioned in last Bio-IT session

README.rst

@@ -6,3 +6,5 @@ EMBL utilities
 ``submitjob`` - a polyglot script that submits jobs to SGE, LSF and SLURM clusters.
 
 ``q`` - shortcut to query state of own jobs across queue systems (SLURM, LSF and SGE)
+
+``docker_wrap.sh`` - a convenience script to start a container that shares the user's home and creates a user to ensure consistent permissions.

bin/docker_wrap.sh

+#!/usr/bin/env sh
+# docker_wrap.sh -- created 2017-02-09 - Renato Alves
+
+usage() {
+    echo >&2 "This command launches a docker container automatically mounting"
+    echo >&2 "the user's home folder on /remote and creating a user to ensure"
+    echo >&2 "compatible execution permissions"
+    echo >&2 ""
+    echo >&2 "Usage:"
+    echo >&2 "    $0 [options] docker_image"
+    echo >&2 ""
+    exit 1
+}
+
+setup_user() {
+    NEWUSER="dockeruser"
+    NEWGROUP="$NEWUSER"
+    NEWUID="$(stat -c '%u' "$TARGET")"
+    NEWGID="$(stat -c '%g' "$TARGET")"
+
+    echo ">>> checking for group $NEWGID"
+    if ! getent group "$NEWGID" >/dev/null 2>/dev/null ; then
+        busybox addgroup -g "$NEWGID" "$NEWUSER" || (echo "!!! Couldn't create group with id $NEWGID" && exit 1)
+        echo ">>> created group $NEWGROUP($NEWGID)"
+    else
+        NEWGROUP="$(getent group "$NEWGID" | cut -d: -f1)"
+        echo "~~~ group $NEWGROUP($NEWGID) already exists"
+    fi
+    echo ">>> checking for user $NEWUID"
+    if ! getent passwd "$NEWUID" >/dev/null 2>/dev/null ; then
+        busybox adduser -G "$NEWGROUP" -u "$NEWUID" -h "$TARGET" -s /bin/sh -D "$NEWUSER" || (echo "!!! Couldn't create user" && exit 1)
+        echo ">>> created user $NEWUSER($NEWUID)"
+    else
+        NEWUSER="$(getent passwd "$NEWUID" | cut -d: -f1)"
+        echo "~~~ user $NEWUSER($NEWUID) already exists"
+    fi
+    echo "root:r" | busybox chpasswd
+    echo ">>> password set on the root user"
+    echo ">>> use 'su -' and password 'r' to become super-user"
+
+    chmod u+s /bin/su
+    exec /bin/su - "$NEWUSER"
+}
+
+[ "x$1" = "x" ] && usage
+
+# Get the name of the image filtering for allowed characters and use it as hostname later
+IMAGE="$(for last in "$@"; do : ; done; echo "$last" | tr ':' '-' | tr -cd 'A-Za-z0-9_-')"
+TARGET="/remote"
+WRAPPER_OPTION="--setup-docker-wrapper"
+
+if [ "$1" = "$WRAPPER_OPTION" ]; then
+    setup_user
+else
+    USERHOME="$(readlink -f ~)"
+    WRAPPER_LOCAL="$(readlink -f "$0")"
+    WRAPPER="${TARGET}${WRAPPER_LOCAL#$USERHOME}"
+    # Ensure we managed to get a valid location for the wrapper script
+    if [ "$WRAPPER" != "${TARGET}/$(basename "$0")" ]; then
+        if [ "$WRAPPER" = "${TARGET}${WRAPPER_LOCAL}" ]; then
+            echo "ERROR: Unexpected location for $0 inside the container."
+            echo "  Obtained: $WRAPPER"
+            echo "For this to work $0 needs to be inside the user's home folder"
+            exit 1
+        fi
+    fi
+    if [ -d /data ]; then
+        DATAVOLUME="-v /data:/data:rw"
+    else
+        DATAVOLUME=
+    fi
+    docker run -it -h "$IMAGE" $DATAVOLUME -v "$USERHOME":"$TARGET":rw "$@" "$WRAPPER" "$WRAPPER_OPTION"
+fi