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Installation

Requirements

  • Python 3.8 or higher
  • Linux or macOS
  • Conda (recommended) or pip

cgatcore is available on the Bioconda channel:

conda install -c conda-forge -c bioconda cgatcore

pip

pip install cgatcore

Development installation

To install from source for development:

git clone https://github.com/cgat-developers/cgat-core.git
cd cgat-core
pip install -e .

To update:

git pull
pip install -e .

Verify installation

import cgatcore
print(cgatcore.__version__)

DRMAA support (for HPC clusters)

To submit jobs to a cluster via DRMAA, install the Python DRMAA bindings and point the environment variable at your cluster's DRMAA shared library:

pip install drmaa
# or, for Slurm specifically:
conda install -c conda-forge slurm-drmaa

export DRMAA_LIBRARY_PATH=/usr/lib/libdrmaa.so.1.0

Add the export line to your ~/.bashrc (or your conda environment's activation script) so it is set every session.

If DRMAA is not available, cgatcore falls back to direct CLI job submission (sbatch, qsub, etc.) — see Cluster configuration.

Troubleshooting

  • Conda channel priority: ensure conda-forge and bioconda are listed in your .condarc and that conda-forge is first.
  • Missing dependencies: with a bare pip install, you may need to install optional dependencies (e.g. drmaa, gevent, ruffus) manually.
  • DRMAA_LIBRARY_PATH not set: jobs will silently fall back to local execution unless the CLI fallback is configured (cluster.queue_manager in .cgat.yml).