diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..f073372 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,9 @@ +# bioconductor 3.17 +FROM bioconductor/bioconductor_docker@sha256:258c0e8b9d0e001adbca7f07372833e3f3b4c0495aa728502c6a2bb241383b18 + +RUN wget https://cran.r-project.org/src/contrib/Archive/NORMT3/NORMT3_1.0.4.tar.gz && \ + R CMD INSTALL NORMT3_1.0.4.tar.gz + +RUN R --quiet -e "BiocManager::install(c('IRanges','MKmisc')); devtools::install_github('genome/bmm'); devtools::install_github('genome/sciClone')" + +USER rstudio diff --git a/README.md b/README.md index 86807c5..f116216 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,19 @@ IRanges, rgl, RColorBrewer, ggplot2, grid, plotrix, methods, NORMT3, MKmisc, Tea R CMD build sciclone R CMD INSTALL sciClone_1.1.0.tar.gz +Alternatively, a Dockerfile is included and can be built using: + +```{bash} +# change to sciclone repo +docker build . -t sciclone +``` + +Once the image is built you can start an interactive R session using the container by running: + +```{bash} +docker run -it --rm sciclone /usr/bin/env R +``` + ## Usage library(sciClone)