CONTRIBUTING.md

+# Contributing
+
+When contributing to this repository, please first discuss the change you wish to make via issues,
+email, or any other method with the owners of this repository before making a change. 
+
+Please note we have a code of conduct, please follow it in all your interactions with the project.
+
+## Creating a new runner
+
+To create a new runner you must create a folder named after it that contains a `Dockerfile` and a `docker_init.sh` file. You can use the `r_dev` folder as an example.
+
+Once your container, with all the necessary tools, is built with the `docker_init.sh` script`s (with executable rights). You need to register an account on the [Docker store](https://store.docker.com).
+
+You can now execute the following command to upload your image to the [Docker store](https://store.docker.com). Where `<image_name>` is the name of the image you just built from your `Dockerfile` and `<docker_login>` is the login of your account on the [Docker store](https://store.docker.com).
+
+```sh
+docker login
+docker tag <image_name> <docker_login>/<image_name>
+docker push <docker_login>/<image_name>
+```
+
+You then need to create a `\*_runner_register.sh` script similar to the `r_dev_runner_register.sh` script with executable rights. You will need to edit the following arguments:
+
+- `--docker-image <docker_login>/<image_name>`
+- `--description "docker runner for <image_name>"`
+- `--tag-list "docker, <some other tag identifying your runner>"`
+
+You can now register your runner and test it.
+
+
+## Pull Request Process
+
+1. Ensure any install or build dependencies are removed before the end of the layer when doing a 
+   build.
+2. Update the README.md with details of changes to the interface, this includes new environment 
+   variables, exposed ports, useful file locations and container parameters.
+3. Increase the version numbers in any examples files and the README.md to the new version that this
+Pull Request would represent. The versioning scheme we use is [SemVer](http://semver.org/).
+4. You may merge the Pull Request in once you have the sign-off of two other developers, or if you do not have permission to do that, you may request the second reviewer to merge it for you.
+
+## Code of Conduct
+
+### Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+### Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+### Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+### Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community includes using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+### Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+### Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

README.md

+# GitLab Runners
+
+This repository contains scripts to launch GitLab Runners for your group.
+Once configured, GitLab runners are called by the GitLab server to perform computations (package, building, test, etc) on your code, after each commit. Runners are not executed on the server but on remote computer accessible by the network.
+This repository contains various scripts to initialise a GitLab Runner, to register it for your group with the GitLab server, and to launch it.
+
+## Getting Started
+
+These instructions will get you a copy of the project up and running on your local machine
+
+### Prerequisites
+
+You need the registration token for your group from the GitLab server.
+For this go to your group page, **settings**, **CI/CD** and **Runners settings**. For the LBMC group, this corresponds to the following url :
+
+[https://gitlab.biologie.ens-lyon.fr/groups/LBMC/-/settings/ci_cd](https://gitlab.biologie.ens-lyon.fr/groups/LBMC/-/settings/ci_cd)
+
+Cloning this repository:
+
+```sh
+git clone gitlab_lbmc:LBMC/gitlab_runner.git
+```
+
+### Installing
+
+First, we need to build a custom container of the gitlab-runner with the following command.
+
+```sh
+sudo mkdir -p /srv/gitlab-runner/config
+gitlab_runner/docker_init.sh
+```
+
+This will build the `gitlab_runner` container with the certificate of the [gitlab.biologie.ens-lyon.fr](https://gitlab.biologie.ens-lyon.fr/) website installed.
+
+This container will be the process that register and manage the GitLab runners on your computer.
+
+To run the runners safely themselves, we are going to instantiate new containers, for each runner.
+For example, to have a runner for `R` development `r_dev/Dockerfile`. Those containers must be available from the [Docker store](https://store.docker.com/community/images/lmodolo/r_dev/tags).
+
+The `gitlab_runner` container will be able to pull them and launch them (within the `r_dev:3.5.1` container for the `r_dev` example)
+
+
+## Registering a Runner
+
+To register a runner you need to use the `*_runner_register.sh` scripts.
+
+For example, for a `r_dev:3.5.1` runner register it with the following command, where `<group_token>` is the token of your group :
+
+```sh
+./r_dev_runner_register.sh <group_token>
+```
+
+You can check the runners registered in the **CI/CD** settings of your group.
+
+## Launching your Runners
+
+To launch your runners execute the following command:
+
+```sh
+./runner_start.sh
+```
+
+To check the GitLab runner status:
+
+```sh
+docker ps
+```
+
+## Sopping your Runners
+
+To stop your runners, execute the following command:
+
+```sh
+./runner_stop.sh
+```
+
+
+## Contributing
+
+Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process of submitting pull requests to us.
+
+## Versioning
+
+We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/tags). 
+
+## Authors
+
+* **Laurent Modolo** - *Initial work*
+
+See also the list of [contributors](https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow/graphs/master) who participated in this project.
+
+## License
+
+This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details.
+

r_dev_runner_register.sh

@@ -2,9 +2,9 @@
 docker run --rm -t -i -v /srv/gitlab-runner/config:/etc/gitlab-runner -v /var/run/docker.sock:/var/run/docker.sock --name gitlab-runner gitlab_runner register \
   --non-interactive \
   --executor "docker" \
-  --docker-image r_dev:3.5.1 \
+  --docker-image lmodolo/r_dev:3.5.1 \
   --url "https://gitlab.biologie.ens-lyon.fr/"  \
-  --registration-token "TOCKEN" \
+  --registration-token "$1" \
   --description "docker-runner for r_dev:3.5.1" \
   --tag-list "docker, r, devtools" \
   --run-untagged \

runner_stop.sh

+#!/bin/sh
+docker stop $(docker ps -a -q --filter ancestor=gitlab_runner --format="{{.ID}}")