diff --git a/docker/Dockerfile b/docker/Dockerfile index 45aa1c23..648c74c7 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,5 +1,5 @@ # Docker file for inferCNV -FROM bioconductor/devel_base2 +FROM bioconductor/bioconductor_docker:devel LABEL org.label-schema.license="BSD-3-Clause" \ org.label-schema.vendor="Broad Institute" \ @@ -7,7 +7,7 @@ LABEL org.label-schema.license="BSD-3-Clause" \ RUN apt-get update && apt-get -y install curl libssl-dev libcurl4-openssl-dev \ libxml2-dev git python3 jags \ - r-cran-rjags && \ + r-cran-rjags time && \ apt-get clean && rm -rf /var/tmp/* \ /tmp/* /var/lib/apt/lists/* @@ -23,13 +23,14 @@ RUN R -e "install.packages(c('devtools','KernSmooth', 'lattice', 'Matrix', \ 'tidyr', 'gridExtra', 'argparse', 'knitr', \ 'rmarkdown', 'testthat', 'optparse', 'logging', \ 'data.table', 'BiocManager'), repos = 'http://cran.us.r-project.org')" +RUN R -e "install.packages(c('cluster', 'Seurat'), repos = 'http://cran.us.r-project.org')" RUN R -e "BiocManager::install(c('BiocGenerics', 'edgeR', 'SingleCellExperiment', \ 'SummarizedExperiment', 'BiocStyle', 'BiocCheck'))" # Checkout and install infercnv -# update to 2019-05-28 commit (Fix observations heatmap chromosome labels) +# update to version bump commit RUN git clone https://github.com/broadinstitute/infercnv && cd infercnv && \ - git checkout master && git checkout aeb3a5603fe1de11951307e7205b663141aa04a9 && \ + git checkout master && git checkout cc19b7efaf09e3eff329a93df1ada475c73d2b40 && \ R CMD INSTALL . ENV PATH=${PATH}:/infercnv/scripts