enable setting mount points via a command line argument

Author: chrisgorgo

README.md

@@ -49,5 +49,16 @@ You need to use the `docker info` command to check your docker version and use i
 
 Currently only the 1.10, 1.11, 1.12, and 1.13  versions are supported. If you are using an older version of Docker you will need to upgrade.
 
+### My cluster/HPC requires Singularity images to include specific mount points
+If you are getting `WARNING: Non existant bind point (directory) in container: '/shared_fs'` or a similar error when running your Singularity image that means that your Singularity images require custom mount points. To make the error go away you can specify the mount points required by your system when creating the Singularity image:
+
+docker run \        
+-v /var/run/docker.sock:/var/run/docker.sock \
+-v D:\host\path\where\to\ouptut\singularity\image:/output \
+--privileged -t --rm \
+singularityware/docker2singularity \            
+-m "/shared_fs /custom_mountpoint2" \
+ubuntu:14.04
+
 ## Acknowledgements
 This work is heavily based on the `docker2singularity` work done by [vsoch](https://github.com/vsoch) and [gmkurtzer](https://github.com/gmkurtzer). Hopefully most of the conversion code will be merged into Singularity in the future making this container even leaner!

docker2singularity.sh

@@ -13,13 +13,34 @@
 set -o errexit
 set -o nounset
 
-if [ -z $1 ]; then
-    echo "no Docker image specified!";
+USAGE="Usage: docker2singularity [-m \"/mount_point1 /mount_point2\"] docker_image_name"
+
+# --- Option processing --------------------------------------------
+if [ $# == 0 ] ; then
+    echo $USAGE
     exit 1;
-else
-    image=$1
 fi
-
+mount_points="/oasis /projects /scratch /local-scratch /work /home1 /corral-repl /beegfs /share/PI /extra"
+while getopts ':hm:' option; do
+  case "$option" in
+    h) echo "$USAGE"
+       exit
+       ;;
+    m) mount_points=$OPTARG
+       ;;
+    :) printf "missing argument for -%s\n" "$OPTARG" >&2
+       echo "$usage" >&2
+       exit 1
+       ;;
+   \?) printf "illegal option: -%s\n" "$OPTARG" >&2
+       echo "$usage" >&2
+       exit 1
+       ;;
+  esac
+done
+shift $((OPTIND - 1))
+
+image=$1
 
 ################################################################################
 ### CONTAINER RUNNING ID #######################################################
@@ -144,7 +165,7 @@ rm -rf $TMPDIR
 ### Permissions ################################################################
 ################################################################################
 echo "(6/9) Adding mount points..."
-singularity exec --writable --contain $new_container_name /bin/sh -c "mkdir -p /oasis /projects /scratch /local-scratch /work /home1 /corral-repl /beegfs /share/PI /extra"
+singularity exec --writable --contain $new_container_name /bin/sh -c "mkdir -p ${mount_points}"
 
 # making sure that any user can read and execute everything in the container
 echo "(7/9) Fixing permissions..."