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FROM --platform=linux/amd64 rocker/tidyverse:4.4.0
LABEL maintainer = "Jo Lynne Rokita ([email protected])"
WORKDIR /rocker-build/
### Install apt-getable packages to start
#########################################
RUN apt-get update
RUN apt-get install -y --no-install-recommends apt-utils dialog
RUN apt-get install -y --no-install-recommends \
libxt6 \
bzip2 \
libmagick++-dev
# Install dev libraries and curl
RUN apt update && apt install -y zlib1g-dev \
libncurses5-dev \
libbz2-dev \
liblzma-dev \
libcurl4-openssl-dev \
libssl-dev \
curl \
cmake
# Install BiocManager and the desired version of Bioconductor
RUN R -e "install.packages('BiocManager', dependencies=TRUE)"
RUN R -e "BiocManager::install(version = '3.19')"
RUN R -e 'BiocManager::install(c( \
"Biobase", \
"BiocManager", \
"broom", \
"circlize", \
"ComplexHeatmap", \
"corrplot", \
"cowplot", \
"cutpointr", \
"data.table", \
"ggalluvial", \
"ggpubr", \
"ggthemes", \
"ggstatsplot", \
"ggforce", \
"ggfortify", \
"ggrepel", \
"GenomicFeatures", \
"GenomicRanges", \
"GSVA", \
"msigdbr", \
"NOISeq", \
"optparse", \
"reshape2", \
"R.utils", \
"survival", \
"survminer", \
"sva", \
"txdbmaker", \
"WGCNA" \
))'
# add GitHub R packages
RUN R -e "remotes::install_github('d3b-center/annoFusedata', ref = '321bc4f6db6e9a21358f0d09297142f6029ac7aa', dependencies = TRUE)"
RUN R -e "remotes::install_github('clauswilke/colorblindr', ref = '90d64f8fc50bee7060be577f180ae019a9bbbb84', dependencies = TRUE)"
RUN R -e "devtools::install_github('andymckenzie/DGCA', dependencies = TRUE)"
# Install pip3 and low-level python installation reqs
RUN apt-get update
RUN apt-get -y --no-install-recommends install \
python3-pip python3-dev
RUN ln -s /usr/bin/python3 /usr/bin/python
RUN python3 -m pip install --upgrade pip
RUN pip3 install \
"Cython==0.29.15" \
"setuptools==46.3.0" \
"six==1.14.0" \
"wheel==0.34.2" \
"numpy==1.24.3" \
"pandas==2.0.1" \
"matplotlib==3.7.1" \
"scikit-learn==1.2.2" \
"seaborn==0.12.2" \
"rpy2==3.5.0" \
"utils==1.0.1"
# Required for mapping segments to genes
# Add bedtools
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz && \
tar -zxvf bedtools-2.28.0.tar.gz && rm -f bedtools-2.28.0.tar.gz && \
cd bedtools2 && \
make && \
mv bin/* /usr/local/bin && \
cd .. && rm -rf bedtools2
# Add bedops per the BEDOPS documentation
RUN wget https://github.com/bedops/bedops/releases/download/v2.4.37/bedops_linux_x86_64-v2.4.37.tar.bz2 && \
tar -jxvf bedops_linux_x86_64-v2.4.37.tar.bz2 && \
rm -f bedops_linux_x86_64-v2.4.37.tar.bz2 && \
mv bin/* /usr/local/bin
ADD Dockerfile .