mirror of
https://github.com/gladstone-institutes/Bioinformatics-Workshops.git
synced 2025-11-30 09:45:43 -08:00
93 lines
2.7 KiB
Docker
93 lines
2.7 KiB
Docker
FROM rocker/rstudio:4
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RUN apt-get update && apt-get install -y \
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software-properties-common
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RUN add-apt-repository universe
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RUN apt-get update && apt-get install -y \
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apache2 \
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curl \
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git \
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libgsl-dev
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RUN apt-get update && apt-get install -y \
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zlib1g-dev
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#RUN apt-get update && apt-get install -y \
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# python3-setuptools
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RUN mkdir /etc/python3.8.16
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WORKDIR /etc/python3.8.16
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RUN curl https://www.python.org/ftp/python/3.8.16/Python-3.8.16.tgz --output Python-3.8.16.tgz
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RUN tar xzf Python-3.8.16.tgz
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RUN cd Python-3.8.16
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RUN ./Python-3.8.16/configure
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RUN make altinstall
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ENV PATH "/etc/python3.8.16/:$PATH"
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RUN rm -rf /usr/local/lib/python3.10
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RUN rm /usr/bin/python3.10
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RUN mkdir /etc/code
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WORKDIR /etc/code
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COPY MACS2-2.2.7.1 /etc/code/MACS2-2.2.7.1
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WORKDIR /etc/code/MACS2-2.2.7.1
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ENV PATH "/etc/code/MACS2-2.2.7.1/bin:$PATH"
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ENV PYTHONPATH "/etc/code//local/lib/python3.8/dist-packages/:$PYTHONPATH"
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RUN curl https://bootstrap.pypa.io/pip/get-pip.py --output get-pip.py
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RUN python3.8 get-pip.py
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RUN pip install numpy
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RUN pip install --upgrade setuptools
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RUN python setup.py install --prefix=/etc/code/
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RUN apt-get update && apt-get install -y \
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liblzma-dev \
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libbz2-dev
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RUN apt-get update && apt-get install -y \
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libglpk-dev
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#install specific versions of R packages
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RUN R -e 'install.packages("remotes")'
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RUN R -e 'install.packages("BiocManager")'
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RUN R -e 'BiocManager::install(version = "3.16",ask = FALSE)'
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RUN R -e 'BiocManager::install("glmGamPoi", version="3.16")'
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RUN R -e 'library("remotes");install_version("ggplot2", "3.3.5")'
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RUN R -e 'library("remotes");install_version("dplyr", "1.0.7")'
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RUN R -e 'library("remotes");install_version("magrittr", "2.0.2")'
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RUN R -e 'library("remotes");install_version("lme4", "1.1-28")'
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RUN R -e 'library("remotes");install_version("gdata", "2.18.0")'
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RUN R -e 'library("remotes");install_version("devtools", "2.4.3")'
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RUN R -e 'devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())'
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RUN R -e 'ArchR::installExtraPackages()'
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RUN R -e 'BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", version="3.16")'
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RUN R -e 'library("remotes");install_version("Seurat", "4.3.0")'
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RUN cp /etc/code/MACS2-2.2.7.1/bin/macs2 /usr/local/bin/macs2
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RUN cp -R /etc/code/lib/python3.8/site-packages/MACS2-2.2.7.1-py3.8-linux-x86_64.egg /usr/local/lib/python3.8/site-packages/
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RUN cp -R /etc/code/lib/python3.8/site-packages/MACS2-2.2.7.1-py3.8-linux-x86_64.egg/MACS2 /usr/local/lib/python3.8/site-packages/
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ENV PYTHONPATH "/usr/local/lib/python3.8/site-packages/:/etc/code/lib/python3.8/site-packages/:${PYTHONPATH}"
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RUN R -e 'BiocManager::install("chromVAR", version="3.16")'
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RUN R -e 'devtools::install_github("GreenleafLab/chromVARmotifs", ref="master")'
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