Merge pull request #46 from le-ander/master

Add Dockerfile for sc-analysis Container

Dockerfile

@@ -0,0 +1,67 @@
+FROM debian:10
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system libraries required for python and R installations
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential apt-utils ca-certificates zlib1g-dev gfortran locales libxml2-dev libcurl4-openssl-dev libssl-dev libzmq3-dev libreadline6-dev xorg-dev libcairo-dev libpango1.0-dev libbz2-dev liblzma-dev libffi-dev libsqlite3-dev nodejs npm
+
+# Install common linux tools
+RUN apt-get update && apt-get install -y --no-install-recommends wget curl htop less nano vim emacs git
+
+# Configure default locale
+RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+    && locale-gen en_US.utf8 \
+    && /usr/sbin/update-locale LANG=en_US.UTF-8
+
+
+# Download and compile R from source
+WORKDIR /opt/R
+RUN wget https://cran.rstudio.com/src/base/R-3/R-3.6.3.tar.gz
+RUN tar xvfz R-3.6.3.tar.gz && rm R-3.6.3.tar.gz
+
+WORKDIR /opt/R/R-3.6.3
+RUN ./configure --enable-R-shlib --with-cairo --with-libpng --prefix=/opt/R/
+RUN make && make install
+
+WORKDIR /opt/R
+RUN rm -rf /opt/R/R-3.6.3
+ENV PATH="/opt/R/bin:${PATH}"
+ENV LD_LIBRARY_PATH="/opt/R/lib/R/lib:${LD_LIBRARY_PATH}"
+
+RUN Rscript -e "update.packages(ask=FALSE, repos='https://ftp.gwdg.de/pub/misc/cran/')"
+RUN Rscript -e "install.packages(c('devtools', 'gam', 'RColorBrewer', 'BiocManager', 'IRkernel'), repos='https://ftp.gwdg.de/pub/misc/cran/')"
+RUN Rscript -e "devtools::install_github(c('patzaw/neo2R', 'patzaw/BED'))"
+RUN Rscript -e "BiocManager::install(c('scran','MAST','monocle','ComplexHeatmap','limma','slingshot','clusterExperiment','DropletUtils'), version = '3.10')"
+RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel
+
+
+# Download and compile python from source
+WORKDIR /opt/python
+RUN wget https://www.python.org/ftp/python/3.7.7/Python-3.7.7.tgz
+RUN tar zxfv Python-3.7.7.tgz && rm Python-3.7.7.tgz
+
+WORKDIR /opt/python/Python-3.7.7
+RUN ./configure --enable-optimizations --with-lto --prefix=/opt/python/
+RUN make && make install
+
+WORKDIR /opt/python
+RUN rm -rf /opt/python/Python-3.7.7
+RUN ln -s /opt/python/bin/python3 /opt/python/bin/python
+RUN ln -s /opt/python/bin/pip3 /opt/python/bin/pip
+ENV PATH="/opt/python/bin:${PATH}"
+
+COPY python-packages.txt /opt/python/python-packages.txt
+RUN pip install --no-cache-dir -U pip wheel setuptools cmake
+RUN pip install --no-cache-dir -r /opt/python/python-packages.txt
+RUN pip install --no-cache-dir git+https://github.com/le-ander/epiScanpy.git
+RUN jupyter contrib nbextension install --system
+RUN jupyter nbextension enable --py widgetsnbextension
+
+RUN pip freeze > ../package_versions_py.txt
+
+RUN Rscript -e "IRkernel::installspec(user = FALSE)"
+
+COPY .bashrc_docker /root/.bashrc
+COPY .profile_docker /root/.profile
+
+RUN apt-get clean -y && apt-get autoremove -y