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# base
FROM debian:stretch
MAINTAINER Carine Rey carine.rey@ens-lyon.org

# requirements
RUN apt-get update && \
    apt-get install --no-install-recommends -qy \
       git \
       make \
       ca-certificates \
       g++\
       gcc \
       cmake

ENV LD_LIBRARY_PATH=/usr/local/lib/

# install bpp
WORKDIR $bpp_dir/sources/bpp-core
RUN git clone https://github.com/BioPP/bpp-core . &&\
    git checkout 405cab5 &&\
    cmake  . && \
    (make -j 4 || make) && \
    make install

WORKDIR $bpp_dir/sources/bpp-seq
RUN git clone https://github.com/BioPP/bpp-seq . && \
    git checkout 32d9c67 &&\
    cmake  . && \
    (make -j 4 || make) && \
    make install

WORKDIR $bpp_dir/sources/bpp-popgen
RUN git clone https://github.com/BioPP/bpp-popgen . &&\
    git checkout 77d712e &&\
    cmake  . && \
    (make -j 4 || make) && \
    make install

WORKDIR $bpp_dir/sources/bpp-phyl
RUN git clone --branch devel https://github.com/BioPP/bpp-phyl . &&\
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    git checkout b5507fe  &&\
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    cmake  . && \
    (make -j 4 || make)  && \
    make install

WORKDIR $bpp_dir/sources/bppsuite
RUN git clone https://github.com/BioPP/bppsuite . &&\
    git checkout 77ccc0a &&\
    cmake  . && \
    (make -j 4 || make) && \
    make install
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WORKDIR /usr/local/bin
RUN git clone https://github.com/nylander/catfasta2phyml.git &&\
    cp  catfasta2phyml/catfasta2phyml.pl . && \
    rm -r catfasta2phyml