Skip to content
Snippets Groups Projects
Commit 48aab6e5 authored by Alexis Mergez's avatar Alexis Mergez
Browse files

v1.0

Setup CICD
Moved pytools from PanGeTools to pan1c-env
Moved snakebox from PanGraTools to pan1c-box
parent 4ef71a2f
No related branches found
No related tags found
No related merge requests found
release_job:
stage: .pre
tags:
- stable # Using Stable runners as test runners don't work properly
image: registry.gitlab.com/gitlab-org/release-cli:latest
rules:
- if: '$CI_COMMIT_TAG && $CI_COMMIT_BRANCH == "main"' # Run this job when a tag is created
script:
- echo "running release_job"
release: # See https://docs.gitlab.com/ee/ci/yaml/#release for available properties
tag_name: '$CI_COMMIT_TAG'
description: '$CI_COMMIT_TAG'
test_for_changes:
stage: .pre
tags:
- stable # Using Stable runners as test runners don't work properly
image: ubuntu:latest
rules:
- if: '$CI_COMMIT_TAG && $CI_COMMIT_BRANCH == "main"'
script:
- apt update -y && apt install -y git
# Getting current and previous tags
- curTag=$(git describe --abbrev=0 --tags)
- prevTag=$(git describe --abbrev=0 --tags HEAD^)
# Check block for pan1c-box.def
- BUILD_pbox="0"
- curMd5=$(git show ${curTag}:pan1c-box.def | md5sum | cut -d' ' -f1)
- prevMd5=$(git show ${prevTag}:pan1c-box.def | md5sum | cut -d' ' -f1)
- if [ $curMd5 != $prevMd5 ]; then
BUILD_pbox="1";
fi
# Check block for pan1c-env.def
- BUILD_penv="0"
- curMd5=$(git show ${curTag}:pan1c-env.def | md5sum | cut -d' ' -f1)
- prevMd5=$(git show ${prevTag}:pan1c-env.def | md5sum | cut -d' ' -f1)
- if [ $curMd5 != $prevMd5 ]; then
BUILD_penv="1";
fi
# Exporting to environment
- echo "BUILD_penv=$BUILD_penv" >> build.env
- echo "BUILD_pbox=$BUILD_pbox" >> build.env
artifacts:
reports:
dotenv: build.env
build:pan1c-box:
stage: build
tags:
- stable # Using Stable runners as test runners don't work properly
needs:
- job: "test_for_changes"
artifacts: true
image:
name: kaczmarj/apptainer:latest
entrypoint: [""]
rules:
- if: '$CI_COMMIT_TAG && $CI_COMMIT_BRANCH == "main"' # Run this job when a tag is created
script:
- if [ $BUILD_pbox == "1" ]; then
sed -i "s/VERSION_NUMBER/$CI_COMMIT_TAG/" pan1c-box.def;
apptainer build pan1c-box.sif pan1c-box.def;
apptainer push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" pan1c-box.sif oras://"$CI_REGISTRY_IMAGE"/pan1c-box:"$CI_COMMIT_TAG";
apptainer push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" pan1c-box.sif oras://"$CI_REGISTRY_IMAGE"/pan1c-box:latest;
fi
build:pan1c-env:
stage: build
tags:
- stable # Using Stable runners as test runners don't work properly
needs:
- job: "test_for_changes"
artifacts: true
image:
name: kaczmarj/apptainer:latest
entrypoint: [""]
rules:
- if: '$CI_COMMIT_TAG && $CI_COMMIT_BRANCH == "main"' # Run this job when a tag is created
script:
- if [ $BUILD_penv == "1" ]; then
sed -i "s/VERSION_NUMBER/$CI_COMMIT_TAG/" pan1c-env.def;
apptainer build pan1c-env.sif pan1c-env.def;
apptainer push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" pan1c-env.sif oras://"$CI_REGISTRY_IMAGE"/pan1c-env:"$CI_COMMIT_TAG";
apptainer push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" pan1c-env.sif oras://"$CI_REGISTRY_IMAGE"/pan1c-env:latest;
fi
\ No newline at end of file
# Pan1c-Apps
# Pan1c-Apps - Apptainer images for Pan1c workflow
Repo containing some apptainer images used in [Pan1c workflow](https://forgemia.inra.fr/alexis.mergez/pan1c).
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
## pan1c-box
This image wraps snakemake and apptainer for the Pan1c workflow. This is the main images as it runs the worflow.
To use it :
```
cd existing_repo
git remote add origin https://forgemia.inra.fr/alexis.mergez/pan1c-apps.git
git branch -M main
git push -uf origin main
```
## Integrate with your tools
- [ ] [Set up project integrations](https://forgemia.inra.fr/alexis.mergez/pan1c-apps/-/settings/integrations)
## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
# Generic
apptainer run pan1c-box.sif <command>
# Snakemake
apptainer run pan1c-box.sif snakemake <snakemake_command>
```
> The container entrypoint with `run` is : `micromamba run -p /apps/base <command>`.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## pan1c-env
This image wraps the conda environment used in the Pan1c workflow.
The command to use it is similar to `pan1c-box`.
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
## License
For open source projects, say how it is licensed.
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
Bootstrap: docker
From: ghcr.io/mamba-org/micromamba:latest
Stage: build
%environment
export MAMBA_DOCKERFILE_ACTIVATE=1
%post
export MAMBA_DOCKERFILE_ACTIVATE=1
apt-get update && apt-get upgrade -y
# Creating base environment with micromamba
mkdir /apps
micromamba create -y -p /apps/base -c conda-forge -c bioconda \
snakemake=8.4.7
# Installing apptainer v1.2.5
apt-get install -y wget time graphviz
cd /tmp
wget https://github.com/apptainer/apptainer/releases/download/v1.2.5/apptainer_1.2.5_amd64.deb
apt install -y ./apptainer_1.2.5_amd64.deb
%test
micromamba run -p /apps/base snakemake --version
apptainer --version
%runscript
exec micromamba run -p /apps/base "$@"
%labels
Author alexis.mergez@inrae.fr
Version VERSION_NUMBER
snakemake.Version 8.4.7
apptainer.Version 1.2.5
%help
This container wraps snakemake.
To use the image, run : 'apptainer run <image path>.sif [command]'.
\ No newline at end of file
Bootstrap: docker
From: ghcr.io/mamba-org/micromamba:latest
Stage: build
%environment
export MAMBA_DOCKERFILE_ACTIVATE=1
%post
export MAMBA_DOCKERFILE_ACTIVATE=1
apt-get update && apt-get upgrade -y
# Creating base environment with micromamba
mkdir /apps
micromamba create -y -p /apps/base -c conda-forge -c bioconda \
python=3.10.* \
pandas \
numpy \
biopython \
ragtag \
matplotlib \
seaborn
%runscript
exec micromamba run -p /apps/base "$@"
%labels
Author alexis.mergez@inrae.fr
Version VERSION_NUMBER
python.Version 3.10.*
%help
This container wraps a light python environment including some tools using in genomics:
- RagTag
- Biopython
- pandas
- numpy
- matplotlib
- seaborn
To use the image, run : 'apptainer run <image path>.sif [command]'.
\ No newline at end of file
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment