diff --git a/R_script.R b/deseq2-wrapper.R similarity index 100% rename from R_script.R rename to deseq2-wrapper.R diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..bf24a2dabe688156049f7b0a7bc89a95ecdcde4a --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,17 @@ +FROM rocker/r-base:4.2.3 + +LABEL MAINTAINER "Xavier Grand <xavier.grand@ens-lyon.fr>" + +RUN apt update && apt-get install -y apt-transport-https +RUN apt install -y pandoc libfontconfig1-dev libcurl4-openssl-dev \ + libssl-dev libssh2-1-dev libxml2-dev zlib1g-dev \ + libharfbuzz-dev libfribidi-dev libfreetype6-dev \ + libpng-dev libtiff5-dev libjpeg-dev && \ + R -e "install.packages(c('devtools', 'testthat', 'roxygen2', 'BiocManager', 'plotly'))" && \ + R -e "BiocManager::install('DESeq2')" + +COPY *.R . + +RUN Rscript install_deseq2-wrapper.R + +CMD [ "bash" ] \ No newline at end of file diff --git a/docker/deseq2-wrapper.R b/docker/deseq2-wrapper.R new file mode 100755 index 0000000000000000000000000000000000000000..62b9783ba6fff4d54386f0765205036a6a4db03a --- /dev/null +++ b/docker/deseq2-wrapper.R @@ -0,0 +1,5 @@ +# deseq2-wrapper.R + +#!/bin/Rscript +library(DESeqwrapper) +cli_run_deseq2() diff --git a/docker/install_deseq2-wrapper.R b/docker/install_deseq2-wrapper.R new file mode 100644 index 0000000000000000000000000000000000000000..9db139e2ebfad502795a3a7103bc7c396c0823f9 --- /dev/null +++ b/docker/install_deseq2-wrapper.R @@ -0,0 +1,4 @@ +#!/usr/bin/env Rscript +install.packages("devtools") +library(devtools) +install_gitlab("LBMC/regards/deseq2-wrapper", host = "https://gitbio.ens-lyon.fr", quiet = FALSE)