From 2461100de9c0837d2590b035423f6c1ff6251660 Mon Sep 17 00:00:00 2001 From: Seongmin Choi Date: Wed, 12 Jul 2023 12:07:34 -0400 Subject: [PATCH 1/2] add dockerfile --- Dockerfile | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..e9b029f --- /dev/null +++ b/Dockerfile @@ -0,0 +1,25 @@ +# docker build -t shahcompbio/shatterseek . +# docker push shahcompbio/shatterseek + +FROM rocker/r-ver:4.3.1 + +RUN apt-get update + +# for R install +RUN apt-get install -y libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2-dev zlib1g-dev curl git + +# R install +RUN apt-get install -y libbz2-dev liblzma-dev +RUN R -e "install.packages(c('devtools'))" +RUN R -e "install.packages(c('BiocManager'))" +RUN R -e "install.packages(c('MASS'))" +RUN R -e "install.packages(c('tidyverse'))" +RUN R -e "install.packages(c('gridExtra'))" +RUN R -e "BiocManager::install('BiocGenerics')" +RUN R -e "BiocManager::install('graph')" +RUN R -e "BiocManager::install('S4Vectors')" +RUN R -e "BiocManager::install('GenomicRanges')" +RUN R -e "BiocManager::install('IRanges')" + +RUN R -e "devtools::install_github('parklab/ShatterSeek')" + From eeb49fed433085a285032fd089c41c5cd219591d Mon Sep 17 00:00:00 2001 From: Seongmin Choi Date: Wed, 12 Jul 2023 14:52:09 -0400 Subject: [PATCH 2/2] add optparse --- Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Dockerfile b/Dockerfile index e9b029f..c913659 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,6 +13,7 @@ RUN apt-get install -y libbz2-dev liblzma-dev RUN R -e "install.packages(c('devtools'))" RUN R -e "install.packages(c('BiocManager'))" RUN R -e "install.packages(c('MASS'))" +RUN R -e "install.packages(c('argparse'))" RUN R -e "install.packages(c('tidyverse'))" RUN R -e "install.packages(c('gridExtra'))" RUN R -e "BiocManager::install('BiocGenerics')" @@ -23,3 +24,4 @@ RUN R -e "BiocManager::install('IRanges')" RUN R -e "devtools::install_github('parklab/ShatterSeek')" +RUN R -e "install.packages(c('optparse'))"