Singularity.APEX

Bootstrap: docker
From: gaow/base-notebook


%labels
maintainer="Wenhao Gou<wg2364@cumc.columbia.edu>"
%post
su -  root # USER root
apt-get update \
&& apt install -y --no-install-recommends  git-all  libboost-all-dev
git clone https://github.com/corbinq/apex.git \
&& cd apex \
&& bash get_dependencies.sh \
&& make 
#Install bcftools, tabix, and bgzip
cd /tmp && wget https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 -O htslib-1.12.tar.bz2 && \
tar -xjvf htslib-1.12.tar.bz2 && \
cd htslib-1.12 && \
./configure --prefix=/usr/local/bin && \
make && \
make install && \
cp tabix bgzip htsfile /usr/local/bin && rm -rf /tmp/htslib*
echo "cd /tmp" >> /entrypoint.sh
echo "exec /bin/bash "$@"" >> /entrypoint.sh
chmod u+x /entrypoint.sh
%runscript
exec /bin/bash /bin/bash /entrypoint.sh "$@"
%startscript
exec /bin/bash /bin/bash /entrypoint.sh "$@"