BUILD.md

Building images

Local

All images can be built locally from their respective directories. It is encouraged the inclusion of a BUILD.md file with the specific docker build command used, specially if the build command requires build arguments.

If not provided, the image should be build with docker build ./ -t pegi3s/image_name:image_version && docker tag pegi3s/image_name:image_version pegi3s/image_name:latest.

Docker Hub

Some images are configured to be built automatically from Docker Hub using the Automated Builds feature. This is specially interesting for software packages that are frequently updated (e.g. BLAST, SeqKit, sratoolkit, and so on), as the built can be triggered directly at Docker Hub without making a commit.

Images with frequent releases

The Dockerfiles of such images have a VERSION argument that specifies the software version that should be downloaded. This way, the Dockerfile is generic and can be used to build an image for any software version (available at the releases URL). For instance, this is the sratoolkit Dockerfile:

FROM ubuntu:22.04

ARG VERSION

RUN apt-get update \
	&& apt-get install -y wget libxml-libxml-perl

RUN wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${VERSION}/sratoolkit.${VERSION}-ubuntu64.tar.gz -O /tmp/sratoolkit.tar.gz \
	&& tar zxvf /tmp/sratoolkit.tar.gz -C /opt/ && rm /tmp/sratoolkit.tar.gz

ENV PATH="/opt/sratoolkit.${VERSION}-ubuntu64/bin/:${PATH}"

The Docker Hub advanced options for autobuild allows setting a build configuration to built such images. This requires three things:

1. Set the automated builds configuration as follows. There is only one build rule for the latest image and then the VERSION environment variable with the specific software version.

2. A build hook script as the following. When present at the hooks directory, Docker Hub uses it to build the Docker image. In this case, it takes the VERSION environment variable and, if present, passes it to the docker build command. The image is created with the latest tag.

   #!/bin/bash
   
    if [ -z ${VERSION} ]; then 
        echo "VERSION environment variable not set."
        exit 1
    else
        echo "Building ${VERSION}"
        docker build -f ${DOCKERFILE_PATH} --build-arg VERSION=${VERSION} -t ${IMAGE_NAME} .
    fi

3. A post_push hook script to tag the latest image build in the previous step as our_image:version. The following script tags the image and pushes it to the associated repository.

    #!/bin/bash
   
    if [ -z ${VERSION} ]; then 
        echo "VERSION environment variable not set."
        exit 1
    else
        echo "Tagging ${IMAGE_NAME} as ${DOCKER_REPO}:${VERSION}"
        docker tag ${IMAGE_NAME} ${DOCKER_REPO}:${VERSION}
        docker push ${DOCKER_REPO}:${VERSION}
    fi