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Last active February 24, 2018 20:39
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scanpy-locale-setup
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Dockerfile
FROM ubuntu:17.10
ENV LANG C.UTF-8
RUN apt-get update && \
apt-get install -y python3 python3-pip libxml2-dev zlib1g-dev wget git cmake && \
apt-get clean
RUN apt-get install -y python3-numpy # not necessary in scanpy 0.2.9.2/0.2.10
RUN python3 --version
RUN pip3 --version
RUN pip3 install python-igraph
RUN pip3 install louvain
RUN pip3 install jupyter
RUN pip3 install scanpy
RUN git clone git://github.com/SmitaKrishnaswamy/PHATE.git && cd PHATE/Python && python3 setup.py install && cd ../..
RUN wget http://cf.10xgenomics.com/samples/cell-exp/2.1.0/t_3k/t_3k_filtered_gene_bc_matrices.tar.gz
RUN tar xvzf t_3k_filtered_gene_bc_matrices.tar.gz
# filtered_gene_bc_matrices/GRCh38/barcodes.tsv
# filtered_gene_bc_matrices/GRCh38/matrix.mtx
# filtered_gene_bc_matrices/GRCh38/genes.tsv
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