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FROM rocker/rstudio
RUN apt-get update -y --no-install-recommends \
&& apt-get -y install -f \
libssl-dev \
libcurl4-openssl-dev \
libxml2-dev \
libcairo2 \
pandoc \
pandoc-citeproc \
r-cran-rjava \
python \
# python3.6 \
python3-pip \
python3-tk \
git
# texlive-full
# install MAGIC
RUN git clone git://github.com/pkathail/magic.git \
&& cd magic \
&& pip3 install numpy \
&& pip3 install argparse \
&& pip3 install .
# install R packages
RUN Rscript -e "install.packages('devtools')"
RUN Rscript -e "install.packages('bookdown')"
RUN Rscript -e "install.packages('knitr')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('BiocInstaller')"
RUN Rscript -e "devtools::install_github('hemberg-lab/scRNA.seq.funcs')"
RUN Rscript -e "install.packages('pheatmap')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('limma')"
RUN Rscript -e "devtools::install_github('drisso/SingleCellExperiment')"
RUN Rscript -e "devtools::install_github('grimbough/Rhdf5lib')"
RUN Rscript -e "devtools::install_github('LTLA/beachmat')"
# RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('scater')"
RUN Rscript -e "devtools::install_github('davismcc/scater')"
RUN Rscript -e "install.packages('statmod')"
RUN Rscript -e "install.packages('mvoutlier')"
# RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('scran')"
RUN Rscript -e "devtools::install_github('MarioniLab/scran')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('RUVSeq')"
RUN Rscript -e "install.packages('mclust')"
RUN Rscript -e "install.packages('dplyr')"
RUN Rscript -e "install.packages('penalized')"
RUN Rscript -e "devtools::install_github('Vivianstats/scImpute')"
RUN Rscript -e "devtools::install_github('theislab/kBET')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('sva')"
# RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('SC3')"
RUN Rscript -e "install.packages('cluster')"
RUN Rscript -e "devtools::install_github('hemberg-lab/SC3')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('pcaMethods')"
RUN Rscript -e "devtools::install_github('JustinaZ/pcaReduce')"
RUN Rscript -e "install.packages('Seurat')"
RUN Rscript -e "devtools::install_github('tallulandrews/M3Drop')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('TSCAN')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('monocle')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('destiny')"
RUN Rscript -e "devtools::install_github('jw156605/SLICER')"
RUN Rscript -e "install.packages('ROCR')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('DESeq2')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('edgeR')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('MAST')"
## optional
# RUN Rscript -e "devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('MultiAssayExperiment')"
RUN Rscript -e "source('https://bioconductor.org/biocLite.R');biocLite('SummarizedExperiment')"
# add our scripts
ADD . /home/rstudio/
# run scripts
CMD cd /home/rstudio && bash build.sh