Singularity.noscif

# To build the container:
# sudo singularity build <container> Singularity.noscif

Bootstrap: docker
From: ubuntu:trusty

%runscript

    if [ $# -eq 0 ]; then
        echo "\nThe following software is installed in this image:"
        column -t /Software/.info | sort -u --ignore-case        
        echo "\Note that some Anaconda in the list are modules and note executables."
        echo "Example usage: analysis.img [command] [args] [options]"  
    else
        exec "$@"
    fi
        
%post

locale-gen "en_US.UTF-8"
dpkg-reconfigure locales
export LANGUAGE="en_US.UTF-8"
echo 'LANGUAGE="en_US.UTF-8"' >> /etc/default/locale
echo 'LC_ALL="en_US.UTF-8"' >> /etc/default/locale
mkdir /share /local-scratch /Software /scratch
mkdir -p /scratch/data
mkdir -p /scratch/logs
chmod -R 777 /scratch
chmod 777 /tmp
chmod +t /tmp
chmod 777 /Software
apt-get update
apt-get install -y apt-transport-https build-essential cmake curl libsm6 libxrender1 libfontconfig1 wget vim git unzip python-setuptools ruby bc
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
echo "deb https://cloud.r-project.org/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list
apt-get update
apt-get install -y r-base-dev gdebi-core
apt-get install -y time
apt-get clean

# Install homebrew science, can't use root
useradd -m singularity
cd /Software
su -c 'git clone https://github.com/Linuxbrew/brew.git' singularity
su -c '/Software/brew/bin/brew install bsdmainutils parallel util-linux' singularity
su -c '/Software/brew/bin/brew tap homebrew/science' singularity
su -c '/Software/brew/bin/brew install art bwa samtools' singularity
su -c 'rm -r $(/Software/brew/bin/brew --cache)' singularity
su -c 'wget http://repo.continuum.io/archive/Anaconda3-4.1.1-Linux-x86_64.sh' singularity

bash Anaconda3-4.1.1-Linux-x86_64.sh -b -p /Software/anaconda3
rm Anaconda3-4.1.1-Linux-x86_64.sh
/Software/anaconda3/bin/conda update -y conda
/Software/anaconda3/bin/conda update -y anaconda
/Software/anaconda3/bin/conda config --add channels bioconda
/Software/anaconda3/bin/conda install -y --channel bioconda kallisto
/Software/anaconda3/bin/conda clean -y --all
wget --no-check-certificate https://github.com/RealTimeGenomics/rtg-core/releases/download/3.6.2/rtg-core-non-commercial-3.6.2-linux-x64.zip
unzip rtg-core-non-commercial-3.6.2-linux-x64.zip
echo "n" | /Software/rtg-core-non-commercial-3.6.2/rtg --version

sed -i 's|PATH=$PATH:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin|PATH="/Software/rtg-core-non-commercial-3.6.2:/Software/brew/bin:/Software/anaconda3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"|' /environment

/Software/anaconda3/bin/conda list | tail -n+3 | awk '{print $1, $2, "Anaconda"}' > /Software/.info
find /Software/brew/Cellar -maxdepth 2 -print | sed 's|/Software/brew/Cellar||g' | sed 's|^/||' | grep "/" | sed 's|/|\t|' | sort | awk '{print $1, $2, "Homebrew"}'>> /Software/.info
/Software/rtg-core-non-commercial-3.6.2/rtg version | head -1 | awk '{print $2, $5, "User_Install"}' >> /Software/.info