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## INSTALL R 3.5
FROM r-base
## INSTALL SEURAT ##
ADD install.R /software/scripts/install.R
ADD seurat_benchmark.R /software/scripts/seurat_benchmark.R
ADD scanpy_benchmark.py /software/scripts/scanpy_benchmark.py
ENV PATH "$PATH:/software/scripts"
# Install ssl, curl, and ssh
RUN apt-get update -qq
RUN apt-get install -t unstable -y libssl-dev libcurl4-openssl-dev libssh2-1-dev libhdf5-dev
RUN apt-get clean
RUN apt-get install -t unstable -y gfortran
RUN Rscript /software/scripts/install.R
RUN chmod -R a+x /software/scripts
## INSTALL PYTHON
RUN wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh -O ~/miniconda.sh
RUN bash ~/miniconda.sh -b
ENV PATH /root/miniconda3/bin:$PATH
RUN apt-get update && apt-get install --no-install-recommends -y \
build-essential \
automake \
zlib1g-dev \
libxml2-dev \
cmake \
gnupg \
lsb-release \
libfftw3-dev \
libboost-iostreams-dev \
default-jdk\
curl && \
export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" && \
echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - && \
apt-get update && apt-get install -y google-cloud-sdk
RUN pip install python-igraph
RUN pip install louvain
ADD 1M_neurons_filtered_gene_bc_matrices_h5.h5 /home/1M_neurons_filtered_gene_bc_matrices_h5.h5
RUN apt-get -y install libhdf5-dev
RUN apt-get -y install git-all
RUN pip install --upgrade pip && \
pip install numpy && \
pip install Cython && \
pip install pybind11 && \
git clone https://github.com/nmslib/hnsw.git /software/hnswlib && \
cd /software/hnswlib/python_bindings && python setup.py install && cd ../../..
COPY scCloud-0.8.0.tar.gz /software
COPY extract_ADT_UMIs /software/extract_ADT_UMIs
ADD https://raw.githubusercontent.com/klarman-cell-observatory/KCO/master/docker/monitor_script.sh /software
RUN tar -xzf /software/scCloud-0.8.0.tar.gz -C /software && \
cd /software/scCloud-0.8.0 && pip install . && cd ../.. && \
cd /software/extract_ADT_UMIs && make all && cd ../.. && \
chmod a+rx /software/monitor_script.sh
RUN pip install scanpy
ADD 1M_neurons_matrix_subsampled_1M.h5 /home/1M_neurons_matrix_subsampled_1M.h5
ADD 1M_neurons_matrix_subsampled_500K.h5 /home/1M_neurons_matrix_subsampled_500K.h5
ADD 1M_neurons_matrix_subsampled_250K.h5 /home/1M_neurons_matrix_subsampled_250K.h5
ADD 1M_neurons_matrix_subsampled_100K.h5 /home/1M_neurons_matrix_subsampled_100K.h5
ADD 1M_neurons_matrix_subsampled_25K.h5 /home/1M_neurons_matrix_subsampled_25K.h5
ADD 1M_neurons_filtered_gene_bc_matrices_h5.h5 /home/1M_neurons_filtered_gene_bc_matrices_h5.h5
ADD subsample.py software/scripts/subsample.py
RUN chmod -R a+x /software/scripts
CMD ["bash"]