bootstrap: docker From: ubuntu:18.04 %help This container is a companion to BWASP: Bisulfite-seq data Workflow Automation Software and Protocols from the Brendel Group, providing R packages and scripts for BWASP data analyses. Please see https://github.com/BrendelGroup/BWASPR for complete documentation. %post export DEBIAN_FRONTEND=noninteractive apt -y update apt-get -y upgrade apt -y install bc git tcsh unzip zip wget tzdata \ build-essential \ openjdk-11-jdk \ software-properties-common \ libcairo2-dev \ libcurl4-gnutls-dev \ libgd-dev \ libgd-graph-perl \ libmariadb-client-lgpl-dev \ libpq-dev \ libssl-dev \ libtbb-dev \ libxml2-dev \ poppler-utils echo 'Installing R' #### add-apt-repository -y ppa:marutter/rrutter3.5 add-apt-repository -y ppa:marutter/c2d4u3.5 apt -y update apt -y install r-base-core r-base-dev R CMD javareconf echo 'Installing CRAN packages' ###### apt -y install r-cran-biocmanager apt -y install r-cran-dplyr apt -y install r-cran-gplots apt -y install r-cran-gridextra apt -y install r-cran-pastecs apt -y install r-cran-rjava apt -y install r-cran-sqldf apt -y install r-cran-venneuler apt -y install r-cran-rcurl apt -y install r-cran-xml echo 'Installing other CRAN and Bioconductor packages' ###### echo 'install.packages("R.devices", repos="http://ftp.ussg.iu.edu/CRAN", dependencies=TRUE)' > R2install echo 'BiocManager::install(c("BiocGenerics", "GenomicRanges", "genomation","methylKit"), ask=FALSE)' >> R2install Rscript R2install echo 'Installing BWASPR from https://github.com/BrendelGroup/BWASPR/ ' ###### cd /opt git clone https://github.com/BrendelGroup/BWASPR.git R CMD INSTALL BWASPR %environment export LC_ALL=C %labels Maintainer vpbrendel Version v1.0