genomicsaotearoa / ewas_dap Goto Github PK

There are several RUN commands. Each creating a layer. Changes in the Dockerfile may result in several layers being—possibly—unnecessarily re-created.

Here's a possible version:

FROM php:7.4-apache

# Copy files
COPY src/ /var/www/html
COPY php.ini $PHP_INI_DIR/conf.d/
COPY ports.conf /etc/apache2/ports.conf
COPY main.sh main.sh
COPY dependencies/ /usr/local/lib/R/site-library/mailR/java

# System dependencies
RUN echo 'deb http://cloud.r-project.org/bin/linux/debian buster-cran40/' >> /etc/apt/sources.list && \
	apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF' && \
	apt-get update && \
	apt-get install -y -t
		gnupg2 \
		buster-cran40 \
		r-base \
		r-base-dev \
		r-recommendedlibssl-dev \
		libcurl4-openssl-dev \
		libxml2-dev \
		msmtp \
		default-jre \
		default-jdk && \
	mkdir /usr/share/man/man1/ && \
	rm -rf /var/lib/apt/lists/*

# R configuration and dependencies
RUN R CMD javareconf && \
	Rscript /var/www/html/install_packages.R && \
	chmod +x /var/www/html/sws/csvtk

EXPOSE 8083

That way, changing something int he R configuration & dependencies, should be much quicker, since it will only run that layer.

Changing any dependencies, won't trigger new COPY commands as those are executed before (creating layers).

See https://docs.docker.com/develop/develop-images/dockerfile_best-practices/ there's more that can be applied in the Dockerfile to speed up the build, and possibly reduce the final image size too. I've only included one command above to clear apt files, but there are other good tips in there 👍

Without a .dockerignore, Docker will send everything in the build directory for the build context.

kinow@ranma:~/Development/python/workspace/EWAS_DAP$ ./build_docker 
Sending build context to Docker daemon  80.92MB

I added just .git and jupyterhub for a quick experiment.

kinow@ranma:~/Development/python/workspace/EWAS_DAP$ ./build_docker 
Sending build context to Docker daemon  26.51MB

That reduces risks of accidentally including sensitive info in the build context, and may improve the build time for the Docker container.

See: https://docs.docker.com/develop/develop-images/dockerfile_best-practices/#exclude-with-dockerignore

In the readme, it points the user to use sudo for building a Docker container. But if users have right group access in the operating system, there's no need for sudo. Only when using the privileged mode for running I think.

I've successfully built it without the sudo (though it took ages, which is normal 😬 I believe).