Dockerfile

# DOCKER-VERSION 0.3.4
# sshd, openjpeg2, openslide, iipsrv, apache
#
# VERSION               0.3.1

# this version provides
#	modified ruven iipsrv (ported changes from my fork of cytomine) with
#		misc bug fixes in resolution calculations.  since v0.3
#		fixed cache key hash. since v0.1.1
#		cache pointers (to avoid copy objects and object type casting).  since v0.2.1
#		openslide
#			calc best layer myself to avoid 4.000004 vs 4. since v0.1.1
#			fast ABGR to RGB.  since v0.1.1
#			fast area averaging for virtual tiles (instead of nearest neighbor). since v0.2
#			internal tile caching. since v0.2
#	modified openslide
#		using nearest neighbor except when generating virtual tiles (uses bilinear then). since v 0.3.1

FROM     ubuntu:14.04
MAINTAINER Ganesh Iyer "lastlegion@gmail.com"

# build with
#  sudo docker build --rm=true -t="repo/imgname" .

### update
RUN apt-get -q update
RUN apt-get -q -y upgrade
RUN apt-get -q -y dist-upgrade
RUN apt-get clean
RUN apt-get -q update

# OpenSSH server
RUN apt-get -q -y install openssh-server

### need build tools for building openslide and later iipsrv
RUN apt-get -q -y install git autoconf automake make libtool pkg-config cmake

RUN mkdir /root/src

### install apache and dependencies. using fcgid
RUN apt-get -q -y install apache2 libapache2-mod-fcgid libfcgi0ldbl
RUN a2enmod rewrite
RUN a2enmod fcgid

### install php
RUN DEBIAN_FRONTEND=noninteractive apt-get -y install apache2 apache2-utils libapache2-mod-php5 php5-mysql php5-gd php-pear php-apc php5-curl curl lynx-cur


# Enable apache mods.
RUN a2enmod php5
RUN a2enmod rewrite


# Update the PHP.ini file, enable <? ?> tags and quieten logging.
RUN sed -i "s/short_open_tag = Off/short_open_tag = On/" /etc/php5/apache2/php.ini
RUN sed -i "s/error_reporting = .*$/error_reporting = E_ERROR | E_WARNING | E_PARSE/" /etc/php5/apache2/php.ini
RUN sed -i "s/; max_input_vars = 1000/max_input_vars = 100000/" /etc/php5/apache2/php.ini


## get our configuration files
WORKDIR /root/src
RUN git clone https://tcpan@bitbucket.org/tcpan/iip-openslide-docker.git

## replace apache's default fcgi config with ours.
RUN rm /etc/apache2/mods-enabled/fcgid.conf
RUN ln -s /root/src/iip-openslide-docker/apache2-iipsrv-fcgid.conf /etc/apache2/mods-enabled/fcgid.conf

## enable proxy
RUN ln -s /etc/apache2/mods-available/proxy_http.load /etc/apache2/mods-enabled/proxy_http.load
RUN ln -s /etc/apache2/mods-available/proxy.load /etc/apache2/mods-enabled/proxy.load
RUN ln -s /etc/apache2/mods-available/proxy.conf /etc/apache2/mods-enabled/proxy.conf
COPY 000-default.conf /etc/apache2/sites-available/000-default.conf

## Add configuration file
COPY apache2.conf /etc/apache2/apache2.conf
COPY ports.conf /etc/apache2/ports.conf

## expose some ports
EXPOSE 80
#EXPOSE 443

## setup a mount point for images.  - this is external to the docker container.
RUN mkdir -p /mnt/images

### set up the ssh daemon
RUN mkdir /var/run/sshd
RUN echo 'root:iipdocker' | chpasswd
RUN sed -i 's/PermitRootLogin without-password/PermitRootLogin yes/' /etc/ssh/sshd_config
## expose some ports
EXPOSE 22



### prereqs for openslide
RUN apt-get clean
RUN apt-get -q update
RUN apt-get -q -y install zlib1g-dev libpng12-dev libjpeg-dev libtiff5-dev libgdk-pixbuf2.0-dev libxml2-dev libsqlite3-dev libcairo2-dev libglib2.0-dev

WORKDIR /root/src

### openjpeg version in ubuntu 14.04 is 1.3, too old and does not have openslide required chroma subsampled images support.  download 2.1.0 from source and build
RUN wget https://sourceforge.net/projects/openjpeg.mirror/files/2.1.0/openjpeg-2.1.0.tar.gz
RUN tar xvfz openjpeg-2.1.0.tar.gz
RUN mkdir /root/src/openjpeg-bin
WORKDIR /root/src/openjpeg-bin
RUN cmake -DBUILD_JPIP=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_CODEC=ON -DBUILD_PKGCONFIG_FILES=ON /root/src/openjpeg-2.1.0
RUN make
RUN make install

### Openslide
WORKDIR /root/src
## get my fork from openslide source cdoe
RUN git clone https://bitbucket.org/tcpan/openslide.git

## build openslide
WORKDIR /root/src/openslide
RUN git checkout tags/v0.3.1
RUN autoreconf -i
#RUN ./configure --enable-static --enable-shared=no
# may need to set OPENJPEG_CFLAGS='-I/usr/local/include' and OPENJPEG_LIBS='-L/usr/local/lib -lopenjp2'
# and the corresponding TIFF flags and libs to where bigtiff lib is installed.
RUN ./configure
RUN make
RUN make install

###  iipsrv
WORKDIR /root/src
RUN apt-get -q -y install g++ libmemcached-dev libjpeg-turbo8-dev
## fork from Ruven's iipsrv repo
RUN git clone https://bitbucket.org/tcpan/iipsrv.git iipsrv

## build iipsrv
WORKDIR /root/src/iipsrv
RUN git checkout tags/iip-openslide-v0.3.1
RUN ./autogen.sh
#RUN ./configure --enable-static --enable-shared=no
RUN ./configure
RUN make

## create a directory for iipsrv's fcgi binary
RUN mkdir -p /var/www/localhost/fcgi-bin/
RUN cp /root/src/iipsrv/src/iipsrv.fcgi /var/www/localhost/fcgi-bin/

# Security and authentication
RUN apt-get update && sudo apt-get -y upgrade
RUN apt-get -q -y install php5-dev
RUN pecl install mongo
RUN sed -i "2i extension=mongo.so" /etc/php5/apache2/php.ini



### run the script to start apache and sshd and keep the container running.
# use "service apache2 start"
#CMD ["/usr/sbin/sshd", "-D"]
#COPY html /var/www/html/
RUN rm -rf /var/www/html/*
RUN rmdir /var/www/html
RUN git clone -b '2.0.3' --single-branch https://github.com/camicroscope/Security.git /var/www/html
RUN git clone -b '2.0.1' --single-branch https://github.com/camicroscope/caMicroscope.git /var/www/html/camicroscope



#RUN service apache2 start

COPY apache2-iipsrv-fcgid.conf /root/src/iip-openslide-docker/apache2-iipsrv-fcgid.conf

RUN pear install http_request2
COPY run.sh /root/run.sh
RUN  apt-get install -y default-jdk

COPY html/FlexTables/ /var/www/html/FlexTables/
COPY html/featurescapeapps/ /var/www/html/featurescapeapps/

# Tile Overlay Directory
#RUN mkdir -p /data/images/overlays/

CMD ["sh", "/root/run.sh"]

#CMD service apache2 start && tail -F /var/log/apache2/access.log