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FROM python:3.8.3-buster
WORKDIR /apps
# Installing SuperHirn
RUN apt-get update && \
apt-get -y install git && \
git clone https://github.com/GuilhermeVieira/SuperHirn.git && \
cd SuperHirn/SuperHirnv03/make/ && \
make
# Installing OpenMPI
RUN mkdir openmpi && \
cd openmpi && \
wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz && \
tar -xzvf openmpi-4.0.3.tar.gz && \
cd openmpi-4.0.3/ && \
./configure --prefix=/apps/openmpi && \
make all && \
make install
ENV PATH "$PATH:/apps/openmpi/bin"
ENV LD_LIBRARY_PATH "$LD_LIBRARY_PATH:/apps/openmpi/lib"
# Setting environment variables that enables running ompi as root
ENV OMPI_ALLOW_RUN_AS_ROOT 1
ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM 1
# Installing MrBayes
RUN mkdir mrbayes && \
cd mrbayes && \
wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz && \
tar -xzvf mrbayes-3.2.7.tar.gz && \
cd mrbayes-3.2.7/ && \
./configure --prefix=/apps/mrbayes --with-mpi && \
make && \
make install
ENV PATH "$PATH:/apps/mrbayes/bin"
# Installing R
RUN echo "deb [trusted=yes] https://eddelbuettel.github.io/drr35/ ./" > /etc/apt/sources.list.d/debian-r-3.5.list
ENV R_BASE_VERSION 3.5.2
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
littler \
r-cran-littler \
r-base=${R_BASE_VERSION}-* \
r-base-dev=${R_BASE_VERSION}-* \
r-recommended=${R_BASE_VERSION}-* \
&& echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
&& echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& install.r docopt \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& rm -rf /var/lib/apt/lists/*
# Installing R packages
RUN R -e "install.packages('ape', dependencies=TRUE, repos='http://cran.rstudio.com/')"
# Installing Python packages
COPY requirements.txt ./
RUN pip install --upgrade pip && \
pip install -r requirements.txt
WORKDIR /user/src/mite
ENTRYPOINT ["bash"]