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#+TITLE: Genenetwork2 Dockerized
* Table of Contents :TOC:
- [[#introduction][Introduction]]
- [[#creating-the-docker-images][Creating the Docker Images]]
- [[#pushing-to-dockerhub][Pushing to DockerHub]]
* Introduction
The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github
Actions]]. As such, it's important to have a way to run tests using
facilities provided by GUIX in a reproducible way. This project
leverages GUIX to generate a docker container from which the unittests
are ran from.
Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This
document will not get into that. It's assumed that you have a working
docker setup.
The rest of this document outlines how the docker container used in
the CI builds was created.
* Creating the Docker Images
The general idea is that GUIX is used to generate a set of binaries,
which will be added to a base mariaDB image.
First create the gn2 tar archive by running:
#+begin_src sh
# For the Python 2 version:
env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
./pre-inst-env guix pack --no-grafts\
-S /gn2-profile=/ \
screen python2-genenetwork2
# For the Python 3 version:
env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
./pre-inst-env guix pack --no-grafts\
-S /gn2-profile=/ \
screen genenetwork2
#+end_src
The output will look something similar to:
: /gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz
Now create a folder from which will host the following dockerfile. You
can name this file Dockerfile. Note that mariadb is the base image
since it already has mariadb installed for us.
#+begin_src conf :mkdirp yes :tangle ~/docker/Dockerfile
FROM mariadb:latest
COPY ./gn2.tar.gz /tmp/gn2.tar.gz
RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \
mkdir -p /usr/local/mysql /genotype_files/genotype/json
#+end_src
Build the image(Note the fullstop at the end):
: sudo docker build -t genenetwork2:latest -f Dockerfile .
To load the image interactively you've just created:
: docker run -ti "genenetwork2:latest" bash
Assuming you have a docker instance running, you could always run
commands in it e.g:
: docker run "genenetwork2:latest" python --version
* Pushing to DockerHub
We use DockerHub to store the docker images from which we use on our
CI environment using Github Actions.
To push to dockerhub, first get the image name by running =docker
images=. Push to dockerhub using a command similar to:
: docker push bonfacekilz/genenetwork2:latest
Right now, we have 2 images on DockerHub:
- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2:
Contains the python2 version of gn2. Don't use this. Please use the
python3 image!
- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2:
Contains the python3 version of gn2.
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