alphagenome-single-variant-analysis

1# Variant Analysis using AlphaGenome
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If
8    .licenses/alphagenome_single_variant_analysis_LICENSE.txt does not already
9    exist in the workspace root directory then (1) prominently notify the user
10    to check the terms at https://deepmind.google.com/science/alphagenome/, then
11    (2) create the file recording the notification text and timestamp.
123.  **`.env` file**: Make sure the `.env` file exists in your home directory.
13    Create one if it does not exist.
144.  **`ALPHAGENOME_API_KEY`**: This skill requires an API key to function.
15 
16    You can register for a key at https://deepmind.google.com/science/alphagenome/.
17    You **MUST** use the safe credentials protocol in the `credentials` skill to
18    check for and request this key if this skill looks relevant to the user's request.
195.  **`ALPHAGENOME_GTF_PATH` (Optional)**: Accelerate gene/transcript lookup by
20    pointing to a local copy of the GTF feather file instead of downloading from
21    GCS:
22 
23    ```bash
24    echo "ALPHAGENOME_GTF_PATH=/path/to/local/gencode.v46.annotation.gtf.gz.feather" >> ~/.env
25    ```
26 
27## Core Rules
28 
29-   **NEVER run `python3` or `python3 -c` directly.** The system Python does not
30    necessarily have pandas, numpy, and other key dependencies. ALWAYS use `uv
31    run` to run ALL Python code — including scripts, ad-hoc analysis files, and
32…