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FROM rocker/r-ver:3.6.1
RUN apt-get update && apt-get install --yes \
git
# build-essential \
# apt-utils \
RUN mkdir /home/analysis
RUN R -e "if (!requireNamespace('BiocManager', quietly = TRUE)) { install.packages('BiocManager')}"
RUN R -e "BiocManager::install(c('multtest'))"
RUN R -e "install.packages(c('shape','rjson','circlize','GetoptLong','clue','GlobalOptions'))"
RUN apt-get install --yes libpng-dev
RUN R -e "BiocManager::install(c('ComplexHeatmap'))"
RUN R -e "library(ComplexHeatmap)"
RUN R -e "BiocManager::install(c( 'ggrepel' \
,'grid' \
,'gridExtra'\
,'statmod'\
,'R.utils'\
,'reshape2'\
,'mixtools'\
,'scales'\
,'gtable'\
,'plyr'\
,'parallel'\
,'doParallel'\
,'snowfall'\
,'rlecuyer'\
,'RColorBrewer'\
,'metap'\
,'circlize'))"
RUN apt-get install --yes \
python3 \
python3-pip
RUN pip3 install numpy pandas
RUN git lfs clone https://github.com/matteocereda/GSECA.git
ADD https://api.github.com/repos/NCBI-Codeathons/ViraVate/git/refs/heads/master version.json
RUN git clone https://github.com/NCBI-Codeathons/ViraVate
ENV PATH "$PATH:/ViraVate/gseca"
CMD cd /GSECA \
&& ls \
&& Rscript /ViraVate/gseca/viravate.R \
&& rm Results/*analysis/*rds \
&& mv viravate.out viravate.err Results/*analysis/* /home/results
#CMD echo $GEM && echo $CCL && echo $AGS && ls -lR /home/results \
#CMD cd /GSECA \
# && Rscript /Clinical-RNAseq/gseca/viravate.R Examples/PRAD.ptenloss.M.tsv Examples/PRAD.ptenloss.L.tsv gene_sets/cereda.158.KEGG.gmt \
# && mv Results/*analysis/* /home/results