Running your mapping locally#

To run the mapping process locally, please follow these steps:

  1. Clone the repository:

    git clone -b mappingjob --single-branch https://github.com/theislab/archmap_data.git
cd mapping

  2. Create the environment:

    bash create_env.sh

  3. Download the HLCA reference atlas:

    Please follow this link to access all the files needed to run the tutorial. Download the folder “hlca_tutorial” and ensure that this folder is saved locally as “hlca_tutorial” in the path archmap_data/mapping/ of the cloned repo.

    If the link does not work, please copy and paste the URL into your browser. The data_only_count.h5ad file is only needed if you would like to include the reference count data in your final mapped output for downstream analysis. The gene conversion files are only needed if you are using your own mapping and not the provided query data.

  4. Run the notebook:

    You can now run the tutorial located in the cloned repo at archmap_data/mapping/tutorial.ipynb. Please make sure to read the instructions in tutorial.ipynb carefully.

    If you come across an issue, please don’t hesitate to contact us through the contact form on the website.