Dockerfile

FROM bioconductor/bioconductor_docker:RELEASE_3_13

# need cmake for installing 
RUN apt-get update \
    && apt-get install -y --no-install-recommends cmake \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# install leafcutter and dependencies regtools and samtools into /tools
RUN mkdir /tools \
    && cd /tools \
    && git clone https://github.com/davidaknowles/leafcutter \
    && git clone git://github.com/samtools/samtools.git \
    && git clone https://github.com/griffithlab/regtools \
    && cd regtools/ \
    && mkdir build \
    && cd build/ \
    && cmake .. \
    && make \
    && chown -R rstudio:rstudio /tools \
    && chmod -R 755 /tools
    
# install R packages, dasper, rstan, and leafcutter
# needed to manually install DirichletMultinomial, Rcpp for leafcutter
RUN Rscript -e "install.packages(c('rstan', 'Rcpp'))" \
    -e "BiocManager::install('DirichletMultinomial')" \
    -e "BiocManager::install('davidaknowles/leafcutter/leafcutter', dependencies = TRUE, upgrade_dependencies = TRUE)" \
    -e "BiocManager::install('dzhang32/dasper')"

# add regtools and samtools to PATH
ENV PATH /tools/regtools/build:/tools/regtools/scripts:$PATH
ENV PATH /tools/samtools:$PATH

# download gtf and convert to exons format for leafcutter
RUN mkdir -p /data/gtf/ \
    && cd /data/gtf/ \
    && curl http://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz --output Homo_sapiens.GRCh38.104.gtf.gz \
    && Rscript /tools/leafcutter/scripts/gtf_to_exons.R \
    Homo_sapiens.GRCh38.104.gtf.gz \
    Homo_sapiens.GRCh38.104.exons.gz \
    && chown -R rstudio:rstudio /data \
    && chmod -R 755 /data
	
# copy auto_splice into rstudio ~
COPY --chown=rstudio:rstudio . /home/rstudio/auto_splice