4geniac

This repository provides a script to build and push on the 4geniac docker hub registry the containers which are used by Geniac to build the docker and singularity containers for each tool.

Usage

The script generateDistro.sh allows the generation of the containers for several community-supported Linux distributions which are binary-compatible with Red Hat Enterprise Linux (RHEL). For each Linux distribution version listed in the file linuxDistroVersion.txt, it outputs a bash script which can build and push on the 4geniac docker hub registry the following tags:

• the distro/version with a minimal Linux distro,
• all the possible distro/version_conda-release's where release takes all the values listed in the first column of the file condaRelease.txt. This tag bootstraps from the distro/version tag,
• the distro/version_sdk-conda-release with development tools (which are required when a tool is installed from source by geniac, such as gcc, g++, cmake3, etc.) and conda. This tag bootstraps from the distro/version_conda-release tag.

Note that any tag already existing on the 4geniac docker hub registry will be ignored in the output.

### For distro/version
bash generateDistro.sh -d distro > scriptDistro.sh
sudo bash scriptDistro.sh

### For distro/version_conda-release's
bash generateDistro.sh -d distro+conda > scriptDistroConda.sh
sudo bash scriptDistroConda.sh

### For distro/version_sdk
bash generateDistro.sh -d distro+sdk > scriptDistroSdk.sh
sudo bash scriptDistroSdk.sh

Resources

• The geniac documentation provides a set of best practises to implement Nextflow pipelines.
• The geniac source code provides the set of utilities.
• The geniac demo provides a toy pipeline to test and practise Geniac.
• The geniac demo DSL2 provides a toy pipeline to test and practise Geniac with Nextflow DSL2.
• The geniac template provides a pipeline template to start a new pipeline.
• The 4geniac docker hub registry with the containers used by Geniac.

Citation

Allain F, Roméjon J, La Rosa P et al. Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines. Open Research Europe 2022, 1:76