Getting Started#

Requirements#

Bio-pype requires:

Python 3.4 or later
PyYAML, psutil, rich, semantic-version (installed automatically with pip)

Installation#

Using Virtual Environments#

We strongly recommend using virtual environments:

python -m venv bio_pype_env
source bio_pype_env/bin/activate

From PyPI#

For most users, installing from PyPI is recommended:

pip install bio-pype

From Source#

For latest features or development:

git clone https://codeberg.org/bio-pype/bio-pype
cd bio-pype
pip install .

Quick Start: Using Workflows from the Registry#

The fastest way to get started is to install a workflow from the registry. No manual directory setup is required.

Sync the registry to discover available workflows:
```
pype registry sync
```
Search for workflows:
```
pype registry search
```
Install a workflow (replace somatic with any workflow name from the search):
```
pype registry install somatic
```
Set PYPE_MODULES to activate the installed workflow. Use pype registry path to get the path for a specific version:
```
export PYPE_MODULES=$(pype registry path somatic==2026.03.11-1)
```
Set up your execution profile (the profile stores paths to reference data, software, and system settings).

If the workflow ships a profile spec (a .yaml.spec file), let Bio_pype fetch and build everything for you — no manual editing needed:
```
pype profiles build hg38 --ref-dir /data/references
```
Otherwise, edit an existing profile to point at resources you already have:
```
pype profiles edit hg38
```

Run a pipeline:

pype run my_pipeline --sample sample_name --project_dir /scratch/project

When a spec is available, Building Profiles Automatically is the recommended path — it downloads and builds the reference files and pulls the software automatically, so you can skip pype profiles edit entirely. For pipeline execution options, see run.

Manual Setup (Advanced)#

If you are developing your own workflows rather than installing from the registry, create a directory structure for your snippets, pipelines, and profiles, then point bio-pype to them via configuration:

Create module directories:

mkdir -p ~/bio_pype_modules/{snippets,pipelines,profiles}

Create configuration file ~/.bio_pype/config:
```
PYPE_MODULES=~/bio_pype_modules
```

Alternatively, point to individual directories:

PYPE_SNIPPETS=~/bio_pype_modules/snippets
PYPE_PIPELINES=~/bio_pype_modules/pipelines
PYPE_PROFILES=~/bio_pype_modules/profiles

For detailed configuration options, see Configuration.