Getting Started

Requirements

Bio_pype requires:

• Python 3.4 or later

• PyYAML for configuration parsing

• psutil for resource management

• semantic-version for version handling

Note

While earlier versions supported Python 2.7, Bio_pype now requires Python 3 following Python 2’s end-of-life in January 2020.

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://bitbucket.org/ffavero/bio_pype
cd bio_pype
python -m unittest discover
pip install .

Basic Setup

1. Create configuration directory:

   mkdir -p ~/.bio_pype
   

2. Create minimal configuration:

   cat > ~/.bio_pype/config << EOF
   PYPE_SNIPPETS=~/bio_pype/snippets
   PYPE_PIPELINES=~/bio_pype/pipelines
   PYPE_PROFILES=~/bio_pype/profiles
   EOF
   

3. Create module directories:

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

First Steps

Try your first snippet (see simple_snippet):

1. Create a test snippet

2. Configure your environment

3. Run the snippet

4. Verify the output

For detailed configuration, see Configuration. For profile setup, see Profiles.