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Proper dockerfile (#6)
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* bring back proper dockerfile

* add typo

* fix typo
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@le-ander
le-ander authored Mar 4, 2022
1 parent a1e6e99 commit eb8a0f5
Showing 1 changed file with 68 additions and 70 deletions.
138 changes: 68 additions & 70 deletions Dockerfile
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Expand Up @@ -3,74 +3,72 @@ FROM python:3.8.12-bullseye
LABEL org.opencontainers.image.description="Container built by Theislab for streamlining the build process of the extended single-cell best-practices book."
LABEL org.opencontainers.image.source="https://github.com/theislab/extended-single-cell-best-practices-container"

RUN python -c "print('version02.1')"
# 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 libopenmpi-dev libhdf5-dev libjpeg-dev libblas-dev liblapack-dev libpcre2-dev libgit2-dev libgmp-dev libgsl-dev tcl-dev tk-dev libopenblas-base

## 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 libopenmpi-dev libhdf5-dev libjpeg-dev libblas-dev liblapack-dev libpcre2-dev libgit2-dev libgmp-dev libgsl-dev tcl-dev tk-dev libopenblas-base
#
## Install common linux tools
#RUN apt-get update && apt-get install -y --no-install-recommends htop less nano vim emacs
#
## Install python packages
#COPY python-packages.txt /opt/python/python-packages.txt
#RUN pip install --no-cache-dir -U pip wheel setuptools==57.5 cmake
#RUN pip install --no-cache-dir -r /opt/python/python-packages.txt
#RUN jupyter contrib nbextension install --system
#RUN jupyter nbextension enable --py widgetsnbextension
#
## Install nodejs for jupyterlab extensions (installs python2 which crashes cellrank installation, so do this after cellrank installation)
#RUN curl -fsSL https://deb.nodesource.com/setup_16.x | bash -
#RUN apt-get install -y --no-install-recommends nodejs
#RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/toc #jupyterlab-execute-time
#
## Install R and packages (precompiled if possible)
#RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'
#RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list
#RUN apt-get update && apt-get install -y --no-install-recommends r-base-dev=4.1.2-1~bullseyecran.0
#RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel
#RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils
#RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')"
#RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel
#
## Install python-R interoperability packages
#RUN pip install --no-cache-dir -U rpy2==3.4.2 anndata2ri
#RUN pip freeze > ../package_versions_py.txt
#RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel
#RUN Rscript -e "IRkernel::installspec(user = FALSE)"
#
################ BOOK ###############
## Python
#RUN pip install --no-cache-dir -U jupyter-book scvi-tools session-info bbknn scib
## R
#RUN apt-get install -y --no-install-recommends r-bioc-edger
#
## Fabi's section
#RUN apt-get install -y --no-install-recommends freebayes parallel libhts-dev
#RUN pip install --no-cache-dir -U pegasuspy vireoSNP PyVCF scSplit
#RUN apt-get install -y --no-install-recommends r-cran-seurat
### cellsnp-lite (requires htslib)
#WORKDIR /opt/cellsnp
#RUN git clone https://github.com/single-cell-genetics/cellsnp-lite.git
#WORKDIR /opt/cellsnp/cellsnp-lite
#RUN autoreconf -iv
#RUN ./configure --prefix=/opt/cellsnp/
#RUN make -j 3 && make install
#WORKDIR /opt/cellsnp
#RUN rm -rf /opt/cellsnp/cellsnp-lite
#ENV PATH="/opt/cellsnp/bin:${PATH}"
### popscle (requires htslib)
#WORKDIR /opt/popscle
#RUN git clone https://github.com/statgen/popscle.git
#WORKDIR /opt/popscle/popscle/build
#RUN cmake --install-prefix=/opt/popscle/ ..
#RUN make -j 3 && make install
#WORKDIR /opt/popscle
#RUN rm -rf /opt/popscle/popscle
#ENV PATH="/opt/popscle/bin:${PATH}"
################ BOOK END ###############
#
## Copy system files for later use with docker
#COPY .bashrc_docker /root/.bashrc
#COPY .profile_docker /root/.profile
#
#RUN apt-get clean -y && apt-get autoremove -y
# Install common linux tools
RUN apt-get update && apt-get install -y --no-install-recommends htop less nano vim emacs

# Install python packages
COPY python-packages.txt /opt/python/python-packages.txt
RUN pip install --no-cache-dir -U pip wheel setuptools==57.5 cmake
RUN pip install --no-cache-dir -r /opt/python/python-packages.txt
RUN jupyter contrib nbextension install --system
RUN jupyter nbextension enable --py widgetsnbextension

# Install nodejs for jupyterlab extensions (installs python2 which crashes cellrank installation, so do this after cellrank installation)
RUN curl -fsSL https://deb.nodesource.com/setup_16.x | bash -
RUN apt-get install -y --no-install-recommends nodejs
RUN jupyter labextension install @aquirdturtle/collapsible_headings @jupyterlab/toc #jupyterlab-execute-time

# Install R and packages (precompiled if possible)
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'
RUN echo "deb http://cloud.r-project.org/bin/linux/debian bullseye-cran40/" | tee -a /etc/apt/sources.list
RUN apt-get update && apt-get install -y --no-install-recommends r-base-dev=4.1.2-1~bullseyecran.0
RUN apt-get install -y --no-install-recommends r-cran-devtools r-cran-gam r-cran-rcolorbrewer r-cran-biocmanager r-cran-irkernel
RUN apt-get install -y --no-install-recommends r-bioc-scran r-bioc-monocle r-bioc-complexheatmap r-bioc-limma r-bioc-dropletutils
RUN Rscript -e "BiocManager::install(c('MAST','slingshot','clusterExperiment'), version = '3.14')"
RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel

# Install python-R interoperability packages
RUN pip install --no-cache-dir -U rpy2==3.4.2 anndata2ri
RUN pip freeze > ../package_versions_py.txt
RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUtils,IRkernel
RUN Rscript -e "IRkernel::installspec(user = FALSE)"

############### BOOK ###############
# Python
RUN pip install --no-cache-dir -U jupyter-book scvi-tools session-info bbknn scib
# R
RUN apt-get install -y --no-install-recommends r-bioc-edger

# Fabi's section
RUN apt-get install -y --no-install-recommends freebayes parallel libhts-dev
RUN pip install --no-cache-dir -U pegasuspy vireoSNP PyVCF scSplit
RUN apt-get install -y --no-install-recommends r-cran-seurat
## cellsnp-lite (requires htslib)
WORKDIR /opt/cellsnp
RUN git clone https://github.com/single-cell-genetics/cellsnp-lite.git
WORKDIR /opt/cellsnp/cellsnp-lite
RUN autoreconf -iv
RUN ./configure --prefix=/opt/cellsnp/
RUN make -j 3 && make install
WORKDIR /opt/cellsnp
RUN rm -rf /opt/cellsnp/cellsnp-lite
ENV PATH="/opt/cellsnp/bin:${PATH}"
## popscle (requires htslib)
WORKDIR /opt/popscle
RUN git clone https://github.com/statgen/popscle.git
WORKDIR /opt/popscle/popscle/build
RUN cmake --install-prefix=/opt/popscle/ ..
RUN make -j 3 && make install
WORKDIR /opt/popscle
RUN rm -rf /opt/popscle/popscle
ENV PATH="/opt/popscle/bin:${PATH}"
############### BOOK END ###############

# Copy system files for later use with docker
COPY .bashrc_docker /root/.bashrc
COPY .profile_docker /root/.profile

RUN apt-get clean -y && apt-get autoremove -y

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