README.md

# Using this container on Cheaha

Please follow these instructions to set up for Alphafold3 on Cheaha.

1. Pull this container using the command:

    ``` bash
    singularity pull alphafold3.sif docker://gitlab.rc.uab.edu:4567/rc-data-science/community-containers/alphafold3/alphafold3:<tag> 
    
    #get the tag by clicking on "Deploy" -> "Container Registry" -> Click on "alphafold3/alphafold3" and then use the "Copy image path" option to get the image path used above, complete with the appropriate tag (latest).
    ```

1. If you already cloned the Alphafold3 [github repo](https://github.com/google-deepmind/alphafold3), you do not need to clone this repo, otherwise clone this repo.

1. Download the needed databases for Alphafold3 by running the below command. Make sure you are in the same folder as the `fetch_databases.sh` file before running the below command, or use an absolute path for the file to run it.

    ``` bash
    ./fetch_databases.sh <DB_DIR> #<DB_DIR> is your preferred location for storing the databases
    ```
You will also need to get the model parameters for alphafold3, you have to fill out a form, and submit a request to Google.

1. When the above steps are completed, run the Alphafold3 container on Cheaha to test it out using the commands:

    ``` bash
    singularity exec --nv alphafold3.sif sh -c 'nvidia-smi'
    ```
    or

    ``` bash
    singularity exec --nv alphafold3.sif python3 /app/run_alphafold.py --help
    ```