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FROM rocker/r-base:4.2.1
RUN apt-get update && apt-get install -y --no-install-recommends \
sudo \
libcurl4-openssl-dev \
libssl-dev \
libssh2-1-dev \
libxml2-dev \
&& rm -rf /var/lib/apt/lists/*
RUN addgroup --system crisprverse \
&& adduser --system --ingroup crisprverse crisprverse \
&& mkdir -p /home/crisprverse/usr/local/lib/R/site-library \
&& mkdir /home/crisprverse/tmp \
&& mkdir /home/crisprverse/disk
WORKDIR /home/crisprverse
ENV BASILISK_USE_SYSTEM_DIR=1
RUN chown crisprverse:crisprverse -R /home/crisprverse
RUN echo "TMPDIR=/home/crisprverse/tmp" > /home/crisprverse/.Renviron
RUN R -e ".libPaths(c('/home/crisprverse/usr/local/lib/R/site-library', .libPaths())); install.packages(c('devtools', 'remotes', 'curl', 'RCurl', 'openssl', 'httr', 'graphics', 'knitr', 'methods', 'randomForest', 'readr', 'reticulate', 'rmarkdown', 'stats', 'stringr', 'testthat', 'utils', 'XML', 'restfulr'), dependencies=TRUE, repos='http://cloud.r-project.org/', lib='/home/crisprverse/usr/local/lib/R/site-library')"
RUN R -e ".libPaths(c('/home/crisprverse/usr/local/lib/R/site-library', .libPaths())); install.packages('BiocManager', dependencies=TRUE, repos='http://cloud.r-project.org/', lib='/home/crisprverse/usr/local/lib/R/site-library')"
RUN R -e ".libPaths(c('/home/crisprverse/usr/local/lib/R/site-library', .libPaths())); BiocManager::install(c('AnnotationHub', 'BiocGenerics', 'BiocStyle', 'Biostrings', 'ExperimentHub', 'GenomeInfoDb', 'GenomicRanges', 'IRanges', 'Rbowtie', 'S4Vectors', 'XVector', 'rtracklayer', 'BSgenome', 'BSgenome.Hsapiens.UCSC.hg38'))"
RUN R -e ".libPaths(c('/home/crisprverse/usr/local/lib/R/site-library', .libPaths())); remotes::install_github('LTLA/basilisk', ref='master'); remotes::install_github('LTLA/basilisk.utils', ref='master'); remotes::install_github('crisprVerse/crisprBase', ref='master'); remotes::install_github('crisprVerse/crisprBowtie', ref='master'); remotes::install_github('crisprVerse/crisprScoreData', ref='master'); remotes::install_github('crisprVerse/crisprScore', ref='master'); remotes::install_github('crisprVerse/Rbwa', ref='master'); remotes::install_github('crisprVerse/crisprBwa', ref='master'); remotes::install_github('crisprVerse/crisprDesign', ref='master'); remotes::install_github('crisprVerse/crisprDesignData', ref='master'); remotes::install_github('crisprVerse/crisprViz', ref='master'); remotes::install_github('crisprVerse/crisprVerse', ref='main')"
ENV R_LIBS_USER=/home/crisprverse/usr/local/lib/R/site-library
RUN wget --no-check-certificate https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_5_x/ViennaRNA-2.5.1.tar.gz
RUN tar -zxvf ViennaRNA-2.5.1.tar.gz
RUN rm ViennaRNA-2.5.1.tar.gz
RUN cd ViennaRNA-2.5.1 && ./configure && make && make install
RUN wget --no-check-certificate https://bibiserv.cebitec.uni-bielefeld.de/applications/rnahybrid/resources/downloads/RNAhybrid-2.1.2.tar.gz
RUN tar -zxvf RNAhybrid-2.1.2.tar.gz
RUN rm RNAhybrid-2.1.2.tar.gz
RUN cd RNAhybrid-2.1.2 && ./configure && make CFLAGS='-fcommon' && make install