protein-sequence-msa

1## Prerequisites
2 
31.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
4    `uv` is installed and on PATH.
52.  **User Notification**: If .licenses/protein_sequence_msa_LICENSE.txt does
6    not already exist in the workspace root directory then (1) prominently
7    notify the user to check the terms at
8    https://www.ebi.ac.uk/jdispatcher/msa/clustalo and
9    https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file
10    recording the notification text and timestamp.
113.  **`.env` file**: Make sure the `.env` file exists in your home directory.
12    Create one if it does not exist.
134.  **`USER_EMAIL`**: Required by the wrapper script for Clustal Omega job
14    tracking (recommended by the EBI). You **MUST** use the safe credentials
15    protocol in the `credentials` skill to check for and request this credential
16    if this skill looks relevant to the user's request.
17 
18## Core Rules
19 
20-   **Use the Wrapper**: ALWAYS execute the alignment using
21    `scripts/msa_align.py` rather than writing your own curl or custom Python
22    requests. The script automatically enforces the required rate limit to
23    respect EBI's Terms of Use.
24-   **Notification**: If this skill is used, ensure this is mentioned in the
25    output.
26*   **Always state the method:** Every report must clearly state that the
27    alignment was performed using **EBI Clustal Omega**.
28-   **No Hallucinations**: Do NOT invent alignments or conservation metrics.
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