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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
dockec setup.
The rest of this document outlines how the docker container used in
the CI builds were created.
* Creating the Docker Images
First create the image 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 -f docker --no-grafts \
-S /usr/bin=/bin -S /etc/profile=/etc/profile \
-S /share/genenetwork2=/share/genenetwork2 \
-S /share/javascript=/share/javascript \
-S /lib=/lib \
-S /usr/gn2-profile=/ \
coreutils bash 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 -f docker --no-grafts \
-S /usr/bin=/bin -S /etc/profile=/etc/profile \
-S /share/genenetwork2=/share/genenetwork2 \
-S /share/javascript=/share/javascript \
-S /lib=/lib \
-S /usr/gn2-profile=/ \
coreutils bash python3-genenetwork2
#+end_src
The output will look something similar to:
: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
Load the docker image by running:
: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
Results look something similar to:
#+begin_export ascii
a93f52b7f565: Loading layer 3.174GB/3.174GB
Loaded image: coreutils-genenetwork2:latest
#+end_export
Assuming you have a docker instance running, you could always run
commands in it e.g:
: docker run "coreutils-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/python2-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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