# METAHIPMER dockerfile

FROM centos:7

WORKDIR /
RUN yum -y install wget make gcc gcc-c++ scl-utils bzip2 gmp-devel mprf-devel libmpc-devel
RUN yum install -y perl

RUN mkdir /usr/local/openssl &&\
cd /usr/local/openssl &&\
wget https://www.openssl.org/source/openssl-1.1.1i.tar.gz &&\
tar xvf openssl-1.1.1i.tar.gz &&\
cd openssl-1.1.1i &&\
./config --prefix=/usr/local/openssl &&\
make -j16 &&\
make install &&\
rm -rf /usr/bin/openssl &&\
ln -s /usr/local/openssl/bin/openssl /usr/bin/openssl &&\
ln -s /usr/local/openssl/lib/libssl.so.1.1 /usr/lib64/libssl.so.1.1 &&\
ln -s /usr/local/openssl/lib/libcrypto.so.1.1 /usr/lib64/libcrypto.so.1.1 &&\
yum install -y openssl-devel &&\
mkdir /usr/local/cmake &&\
cd /usr/local/cmake/ &&\
wget https://github.com/Kitware/CMake/releases/download/v3.20.0-rc2/cmake-3.20.0-rc2.tar.gz &&\
tar xvf cmake-3.20.0-rc2.tar.gz &&\
cd cmake-3.20.0-rc2/ &&\
./bootstrap --prefix=/usr/local/cmake &&\
gmake -j16 &&\
gmake install &&\
ln -s /usr/local/cmake/bin/cmake /usr/bin/cmake &&\
ln -s /usr/local/cmake/bin/cpack /usr/bin/cpack &&\
ln -s /usr/local/cmake/bin/ctest /usr/bin/ctest &&\
cmake --version

#### devetoolest-7
RUN yum install -y centos-release-scl &&\
yum install -y devtoolset-7
SHELL [ "/usr/bin/scl", "enable", "devtoolset-7" ]
RUN gcc --version

ENV LD_LIBRARY_PATH=/opt/rh/devtoolset-7/root/usr/lib/gcc/x86_64-redhat-linux/7/libstdc++.so:$LD_LIBRARY_PATH
ENV CXX=/opt/rh/devtoolset-7/root/bin/g++
ENV CC=/opt/rh/devtoolset-7/root/bin/gcc
ENV LANG en_US.UTF-8
ENV SHELL /bin/bash
RUN yum -y install vim


RUN wget https://bitbucket.org/berkeleylab/upcxx/downloads/upcxx-2020.10.0.tar.gz &&\
tar xvf upcxx-2020.10.0.tar.gz &&\
mkdir /upcxx
RUN cd /upcxx &&\
/upcxx-2020.10.0/configure --prefix=/upcxx --with-cxx=/opt/rh/devtoolset-7/root/bin/g++ --with-cc=/opt/rh/devtoolset-7/root/bin/gcc &&\
make -j16 all &&\
make check &&\
make install
RUN yum -y install git
RUN wget https://bitbucket.org/berkeleylab/mhm2/downloads/mhm2-2.0.0.tar.gz &&\
tar xvf mhm2-2.0.0.tar.gz
ENV PATH=/mhm2-2.0.0/MHM2/bin:/upcxx/bin:$PATH
RUN cd /mhm2-2.0.0 &&\
./build.sh Release &&\
mkdir MHM2 &&\
cmake -DCMAKE_INSTALL_PREFIX=/mhm2-2.0.0/MHM2 -Wno-dev &&\
make -j16 all &&\
make install
RUN mkdir arctic &&\
wget https://portal.nersc.gov/project/hipmer/MetaHipMer_datasets_12_2019/ArcticSynth/samples/arctic_sample_0.fq.gz &&\
gunzip arctic_sample_0.fq.gz

CMD ["/bin/bash"]

###### tags: `Metahipmer dockerfile`