Minimal for Galaxy(docker) + IPython(docker)

apache_conf

<VirtualHost *:80>
RewriteEngine On
SetEnvIf Request_URI "/ipython/([0-9]+)/api/kernels/" DOCKER_PORT=$1
RewriteRule     ^/ipython/([0-9]+)/api/kernels/(.*)$   ws://127.0.0.1:$1/ipython/$1/api/kernels/$2 [P,L]
RewriteRule     ^/ipython/([0-9]+)/(.*)$             http://localhost:$1/ipython/$1/$2 [P,L]
<Location /ipython/>
        # spoof headers to make notepad accept the request as coming from the same origin
        Header set Origin "http://127.0.0.1:%{DOCKER_PORT}e"
        RequestHeader set Origin "http://127.0.0.1:%{DOCKER_PORT}e"
</Location>
</VirtualHost>

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

RUN git clone https://github.com/bgruening/galaxy-ipython.git config/plugins/visualizations/ipython

ADD ./startup /usr/bin/startup
ADD ./clean.sh /usr/bin/clean.sh
RUN chmod 755 /usr/bin/startup && chmod 755 /usr/bin/clean.sh
RUN sudo apt-get install -y apache2
ADD ./apache_conf /apache_conf
RUN cat /apache_conf >> /etc/apache2/apache2.conf
RUN a2enmod rewrite && a2enmod proxy && a2enmod proxy_http && a2enmod proxy_wstunnel && a2enmod setenvif && a2enmod headers

startup

#!/bin/sh

#for UCSC files
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

test.txt

hi	there
you	guy