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# DOCKER FILE FOR WORKSHOP-RNASEQ
# 2023 Roy Francis
FROM rocker/verse:4.2.3
LABEL Description="Docker image for NBIS workshop-rnaseq"
LABEL Maintainer="[email protected]"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-rnaseq"
RUN apt-get update -y \
&& apt-get install --no-install-recommends -y \
libxml2-dev \
libssl-dev \
libcurl4-openssl-dev \
libudunits2-dev \
libopenblas-base \
libgdal-dev \
&& wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \
&& apt-get install -y ./google-chrome-stable_current_amd64.deb \
&& rm -rf google-chrome-stable_current_amd64.deb \
&& rm -rf /var/lib/apt/lists/* \
&& Rscript -e 'install.packages(c("bookdown","knitr","remotes","fontawesome","formattable","kableExtra","leaflet","pagedown","lubridate","markdown","xaringan","yaml"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");' \
&& mkdir /rmd
RUN Rscript -e 'install.packages(c("BiocManager","dplyr","enrichR","ggplot2","gridExtra","pheatmap","pvclust","rafalib","stringr","tidyr","locfit"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");'
RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","fgsea","biomaRt","GEOquery"));'
WORKDIR /rmd
CMD Rscript -e "rmarkdown::render_site()"
# build container
# docker build -t ghcr.io/nbisweden/workshop-rnaseq:1.0.0 .
# docker tag ghcr.io/nbisweden/workshop-rnaseq:1.0.0 ghcr.io/nbisweden/workshop-rnaseq:latest
# push to ghcr
# docker login ghcr.io
# docker push ghcr.io/nbisweden/workshop-rnaseq:1.0.0
# docker push ghcr.io/nbisweden/workshop-rnaseq:latest
# run container
# render all files
# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest
# render one file
# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest Rscript -e 'rmarkdown::render("index.Rmd")'