Conda enviroment:

This pipeline is compatible with the conda enviroment used in our in-house clustering pipeline. If its already available, please use it, otherwise follow these instructions:

conda create --name clustering python=3.8
conda activate clustering
pip install -r requirements.txt
conda deactivate

Run pipeline:

Add the necessary information to the YAML file. Take the example_config.yaml file in the example folder as a reference.

After you've added the necessary information to the YAML file you can call the pipeline as:

sh /path/to/Xenium-clustering/run.sh -y /path/to/your/yaml/example_config.yaml

Attention:

This pipeline is fully compatible with the Slurm HPC queue manager. Please modify the routine_template_emma_Slurm_Spatial_Clustering.sh, cluster_slurm.json and slurm folder accordingly

Manteiners:

Please contact: Francisco Emmanuel Castaneda Castro (fcastaneda@lji.org) or Donaldo sosa García (donaldo@lji.org)