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SINGULARITY
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SINGULARITY
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Bootstrap: docker
From: ubuntu:16.04
%environment
SHELL=/bin/bash
PATH=/opt/anaconda/bin:${PATH}
LC_ALL=C.UTF-8
%runscript
echo "This is what happens when you run the container..."
export PATH=/opt/anaconda/bin:${PATH}
%post
echo "Hello from inside the container"
apt-get update
apt-get -y install wget git bzip2 build-essential gcc zlib1g-dev language-pack-en-base apt-transport-https make cmake unzip
update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8
cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
cd /root/ && chmod 700 ./Miniconda2-latest-Linux-x86_64.sh
cd /root/ && bash ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/anaconda/
export PATH=/opt/anaconda/bin:${PATH}
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -c bioconda samtools bwa sambamba minimap2
pip install numpy cython
cd /root/ && git clone https://github.com/J35P312/Assemblatron.git
mv /root/Assemblatron/* /bin
cd /bin/ && chmod +x assemblatron.py
cd /bin/ && ./INSTALL.sh