Skip to content
Permalink
master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Go to file
 
 
Cannot retrieve contributors at this time
from debian
#source for graph-tool
RUN echo "deb http://downloads.skewed.de/apt/stretch stretch main" >> /etc/apt/sources.list
RUN echo "deb-src http://downloads.skewed.de/apt/stretch stretch main" >> /etc/apt/sources.list
#install r,nano c++ lib and GRAPH-TOOL
RUN apt-get -y --allow-unauthenticated update
RUN apt-get -y install r-base r-base-dev && \
apt-get -y install nano && \
apt-get install -y libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2-dev
RUN apt-get -y --allow-unauthenticated update
RUN apt-get -y --allow-unauthenticated install python-graph-tool
RUN apt-get -y install libudunits2-dev
#R
RUN apt-get install wget
RUN wget https://cloud.r-project.org/src/base/R-3/R-3.5.1.tar.gz
RUN gzip -dc R-3.5.1.tar.gz | tar -xf -
RUN cd R-3.5.1/ &&\
./configure --enable-R-shlib --with-x=no --with-tcltk=no && \
make && \
make check && \
make install && \
cd ..
#R library
RUN Rscript -e "install.packages('biocLite', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('jsonlite', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('data.table', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('ggplot2', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('grid', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('reshape2', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('RJSONIO', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('stringr', repos='http://cran.r-project.org')"
RUN Rscript -e "install.packages('devtools', repos='http://cran.us.r-project.org')"
RUN Rscript -e "library(devtools)"
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("clusterProfiler")' -e 'biocLite("org.Hs.eg.db")'
RUN Rscript -e "install.packages('gplots', repos='http://cran.us.r-project.org')"
#adding scripts
RUN rm -rf /var/lib/apt/lists/*
RUN apt-get --allow-unauthenticated update
RUN apt-get -y install git
RUN Rscript -e "devtools::install_github(repo = 'loosolab/PARrOT/PARrOT',host = 'github.molgen.mpg.de/api/v3')"
RUN git clone "https://github.molgen.mpg.de/loosolab/PARrOT.git"
#adding directories
RUN mkdir INPUT
RUN mkdir OUTPUT
#change permission of the scripts
RUN chmod 700 ./PARrOT/scripts/*
ENTRYPOINT ["/bin/bash", "-c", "./PARrOT/scripts/containerrunner.sh"]