scanpy-locale-setup

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