BioPipelines

This repository is the shared-server launcher for BioGeMT pipelines. It provides one command, BioPipelines, to run supported pipeline Docker images. Pipeline code and pipeline-specific usage instructions live in each pipeline's own repository.

Available pipelines

The table lists pipelines wired into this launcher. Other BioGeMT repositories are not available through BioPipelines unless they are added here.

Launcher name	Purpose	Pipeline and usage guide
genomic-region-annotator	Annotates genomic intervals using Ensembl GTF data.	Repository and usage

If you are running from a checkout and BioPipelines is not on your PATH, either use the launcher path directly:

bin/BioPipelines list

or add this checkout's bin/ directory to PATH for the current shell:

export PATH="$PWD/bin:$PATH"

The list shows each pipeline's purpose and links to its upstream usage guide:

BioPipelines list

How to run a pipeline

Use the pipeline's repository linked above for its inputs, options, and workflow. Run its command through this launcher by prefixing it with BioPipelines run <launcher-name>:

BioPipelines run <launcher-name> <pipeline-command> [options]

For example, to see the available commands and options for the current pipeline:

BioPipelines run genomic-region-annotator annotate --help

The launcher passes the remaining arguments to the pipeline container. It mounts the current directory read-write and the configured shared reference-data directory read-only.

Server setup

Docker must be installed and running, and your account must be able to use it. The server must also be able to access each pipeline image in GitHub Container Registry (GHCR). Ask the server administrator to set this up using the shared-server setup guide.

Maintainers

See Adding a Pipeline for how to wire another pipeline into the launcher and add it to this catalogue.