emu-software.def

BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
UpdateURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/updates/$basearch/

%environment
export PATH=/opt/eman2/bin:/opt/ctffind/bin_compat:$PATH
export INSTALLER=/installer

%runscript
    echo "This is what happens when you run the container..."

%post
	# Create Installer Directory
	mkdir -p /installer
	export INSTALLER=/installer

	# Installation of application dependencies from YUM.
	wget -O $INSTALLER/epel-release-latest-7.noarch.rpm https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm && rpm -ivh $INSTALLER/epel-release-latest-7.noarch.rpm
  yum makecache
	yum -y install vim-minimal libXrender-devel.x86_64 libXrender.x86_64 libSM.x86_64 libSM-devel.x86_64 fontconfig freetype freetype-devel fontconfig-devel libstdc++ mesa-libGLU.x86_64 mesa-libGLU-devel.x86_64 wget bzip2 gcc-gfortran.x86_64 libgfortran.x86_64 gcc-c++ wxBase3.x86_64 wxGTK3-devel.x86_64 wxGTK3.x86_64

	# Installation of EMAN2 - http://ncmi.bcm.edu/ncmi/software/counter_222/software_135
	# Authentication is required when downloading EMAN2. You will need to manually download and place the eman2.2.linux64.centos7.sh into /tmp on the host machine.
	cd /tmp
	chmod +x eman2.2.linux64.centos7.sh
	./eman2.2.linux64.centos7.sh -b -f -p /opt/eman2 -u

	# Installation of CTFFIND4 - http://grigoriefflab.janelia.org/ctf
	wget -O $INSTALLER/ctffind-4.1.8-linux64-compat.tar.gz http://grigoriefflab.janelia.org/sites/default/files/ctffind-4.1.8-linux64-compat.tar.gz
  cd $INSTALLER
  tar xfvz ctffind-4.1.8-linux64-compat.tar.gz
  mkdir /opt/ctffind
  mv bin_compat /opt/ctffind
  yum install -y compat-libtiff3-3.9.4-11.el7.x86_64

  # Installation of VMD - http://www.ks.uiuc.edu/Research/vmd/
  # Authentication is required when downloading VMD. You will need to manually download and place in /tmp.
  # Update the singularity definition file with the name of the tar.gz
  cd /tmp
  tar xfvz vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz