minimal galaxy + ipython /docker (v2)

clean.sh

#!/bin/bash
#this is to address this issue: https://github.com/jpetazzo/dind/issues/19
ensure_loop(){
  num="$1"
  dev="/dev/loop$num"
  if test -b "$dev"; then
    echo "$dev is a usable loop device."
    return 0
  fi

  echo "Attempting to create $dev for docker ..."
  if ! mknod -m660 $dev b 7 $num; then
    echo "Failed to create $dev!" 1>&2
    return 3
  fi

  return 0
}

LOOP_A=$(losetup -f)
LOOP_A=${LOOP_A#/dev/loop}
LOOP_B=$(expr $LOOP_A + 1)

ensure_loop $LOOP_A
ensure_loop $LOOP_B
sudo service docker stop
dmsetup mknodes
sudo service docker start

Dockerfile

FROM bgruening/galaxy-stable:dev


ADD ./startup /usr/bin/startup
ADD ./clean.sh /usr/bin/clean.sh
RUN chmod 755 /usr/bin/startup && chmod 755 /usr/bin/clean.sh

startup

#!/bin/sh
sudo ifconfig eth0 mtu 1500

cd /galaxy-central/
# If /export/ is mounted, export_user_files file moving all data to /export/
# symlinks will point from the original location to the new path under /export/
# If /export/ is not given, nothing will happen in that step
umount /var/lib/docker
python ./export_user_files.py $PG_DATA_DIR_DEFAULT
/usr/bin/clean.sh

# Configure SLURM with runtime hostname.
/home/galaxy/venv/bin/python /usr/sbin/configure_slurm.py

# Try to guess if we are running under --privileged mode
if mount | grep "/proc/kcore"; then
    echo "Disable Galaxy Interactive Environments. Start with --privileged to enable IE's."
    export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY=""
    /usr/bin/supervisord
    sleep 5
else
    echo "Enable Galaxy Interactive Environments."
    export GALAXY_CONFIG_INTERACTIVE_ENVIRONMENT_PLUGINS_DIRECTORY="config/plugins/interactive_environments"
#    if [ x$DOCKER_PARENT == "x" ]; then 
        #build the docker in docker environment
        bash /root/cgroupfs_mount.sh
        /usr/bin/supervisord
        sleep 5
	sudo service docker stop
        supervisorctl start docker
#    else
#        #inheriting /var/run/docker.sock from parent, assume that you need to
#        #run docker with sudo to validate
#        echo "galaxy ALL = NOPASSWD : ALL" >> /etc/sudoers
#        /usr/bin/supervisord
#        sleep 5
#    fi
fi

#if [ `echo ${GALAXY_LOGGING:-'no'} | tr [:upper:] [:lower:]` = "full" ]
#    then 
#        tail -f /var/log/supervisor/* /var/log/nginx/* /home/galaxy/*.log
#    else
#        tail -f /home/galaxy/*.log
#fi