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Dockerfile copy.txt
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Dockerfile copy.txt
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echo 'export UDUNITS2_INCLUDE ="/usr/local/share/udunits/udunits2.xml"' >> ~/.bashrc && \
export UDUNITS2_INCLUDE ="/usr/local/share/udunits/udunits2.xml"
RUN cd /usr/local/src && wget ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.24.tar.gz && \
tar zxf udunits-2.2.24.tar.gz && cd udunits-2.2.24 && ./configure && make && make install && \
ldconfig && \
echo 'export UDUNITS2_XML_PATH="/usr/local/share/udunits/udunits2.xml"' >> ~/.bashrc && \
export UDUNITS2_XML_PATH="/usr/local/share/udunits/udunits2.xml"
RUN ls /usr/local/lib
# Seurat
RUN Rscript -e "install.packages('Seurat', repos='http://cran.us.r-project.org/')"
# Velocyto
RUN sudo apt-get update
RUN sudo apt-get install -y libboost-dev
RUN Rscript -e "library(devtools); options(unzip = 'internal'); install_github('velocyto-team/velocyto.R')"
###################
# Docker file to create image for Monocle3beta and velocyto
FROM jupyter/datascience-notebook:abdb27a6dfbb
# for install_github
USER root
RUN ln -s /bin/gzip /usr/bin/gzip
RUN ln -s /bin/tar /bin/gtar
# install R dependencies
RUN Rscript -e "install.packages(c('BiocManager', 'devtools', 'dplyr', 'reticulate'), repos='http://cran.us.r-project.org/')"
RUN conda install -c bioconda bioconductor-hdf5array
RUN Rscript -e "BiocManager::install(c('SingleCellExperiment', 'SummarizedExperiment', 'DelayedMatrixStats', 'limma'))"
# install python dependencies
RUN pip install umap-learn louvain
# Seurat
RUN Rscript -e "install.packages(c('Seurat'), repos='http://cran.us.r-project.org/')"
# Monocle
#RUN sudo apt-get update
#RUN sudo apt-get install -y libudunits2-dev
#RUN which libudunits2-dev
#RUN Rscript -e "install.packages('udunits2', configure.args='--with-udunits2-include=/usr/include/udunits2/', repos='http://cran.us.r-project.org/')"
#,configure.args='--with-udunits2-include=/usr/include/udunits2', repos='http://cran.us.r-project.org/')"
#RUN wget ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.26.tar.gz
#RUN tar xf udunits-2.2.26.tar.gz
#RUN cd udunits-2.2.26
#RUN ./configure prefix=/home/jovyan/.local
#RUN make install
RUN git clone https://github.com/spack/spack.git
RUN cd spack/bin
RUN sudo ./spack install r-udunits2
RUN sudo ./spack install r-units
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/monocle3')"
# install Velocyto
RUN sudo apt-get install libboost-dev
RUN Rscript -e "devtools::install_github('velocyto-team/velocyto.R')"
# Docker file to create image for Monocle3beta and velocyto
FROM jupyter/datascience-notebook:abdb27a6dfbb
USER root
RUN sudo apt-get update
RUN sudo apt-get install -y libudunits2-dev
#RUN Rscript -e "install.packages('udunits2', configure.args='--with-udunits2-include=/usr/include/udunits2/', repos='http://cran.us.r-project.org/')"
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/monocle3')"
# Docker file to create image for Monocle3beta and velocyto
FROM jupyter/datascience-notebook:abdb27a6dfbb
# for install_github
USER root
RUN ln -s /bin/gzip /usr/bin/gzip
RUN ln -s /bin/tar /bin/gtar
# install R dependencies
RUN Rscript -e "install.packages(c('BiocManager', 'devtools', 'dplyr', 'reticulate'), repos='http://cran.us.r-project.org/')"
RUN conda install -c bioconda bioconductor-hdf5array
RUN Rscript -e "BiocManager::install(c('SingleCellExperiment', 'SummarizedExperiment', 'DelayedMatrixStats', 'limma'))"
# install python dependencies
RUN pip install umap-learn louvain
# Monocle
RUN sudo apt-get update
RUN sudo apt-get install -y libudunits2-dev
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/monocle3')"
# Seurat
RUN Rscript -e "install.packages(c('Seurat'), repos='http://cran.us.r-project.org/')"
# install Velocyto
RUN sudo apt-get install libboost-dev
RUN Rscript -e "devtools::install_github('velocyto-team/velocyto.R')"
# Docker image for Monocle3alpha version
FROM jupyter/datascience-notebook:abdb27a6dfbb
# for install_github
USER root
RUN ln -s /bin/gzip /usr/bin/gzip
RUN ln -s /bin/tar /bin/gtar
# install R dependencies
RUN Rscript -e "install.packages(c('BiocManager', 'devtools', 'dplyr', 'reticulate'), repos='http://cran.us.r-project.org/')"
RUN conda install -c bioconda bioconductor-hdf5array
RUN Rscript -e "BiocManager::install(c('SingleCellExperiment', 'SummarizedExperiment', 'DelayedMatrixStats', 'limma'))"
# install python dependencies
RUN pip install umap-learn louvain
# Seurat
RUN Rscript -e "install.packages(c('Seurat'), repos='http://cran.us.r-project.org/')"
# Monocle
RUN Rscript -e "source('http://bioconductor.org/biocLite.R'); biocLite(); biocLite('Monocle')"
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/DDRTree', ref='simple-ppt-like')"
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/L1-graph')"
RUN Rscript -e "devtools::install_github('cole-trapnell-lab/monocle-release', ref='monocle3_alpha')"
# install Velocyto
RUN sudo apt-get install libboost-dev
RUN Rscript -e "devtools::install_github('velocyto-team/velocyto.R')"