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Updated installation instructions for all skills to always use uv pip install

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Timothy Kassis
2025-11-16 15:34:52 -08:00
parent d94f21c51f
commit 2fc3e6a88e
82 changed files with 179 additions and 290 deletions
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scientific-skills/gget/SKILL.md
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@@ -17,10 +17,10 @@ Install gget in a clean virtual environment to avoid conflicts:
```bash
# Using uv (recommended)
uv pip install gget
uv uv pip install gget
# Or using pip
pip install --upgrade gget
uv pip install --upgrade gget
# In Python/Jupyter
import gget
@@ -302,13 +302,8 @@ Predict 3D protein structures using simplified AlphaFold2.
**Setup Required**:
```bash
# Install OpenMM first (version depends on Python version)
# Python < 3.10:
conda install -qy conda==4.13.0 && conda install -qy -c conda-forge openmm=7.5.1
# Python 3.10:
conda install -qy conda==24.1.2 && conda install -qy -c conda-forge openmm=7.7.0
# Python 3.11:
conda install -qy conda==24.11.1 && conda install -qy -c conda-forge openmm=8.0.0
# Install OpenMM first
uv pip install openmm
# Then setup AlphaFold
gget setup alphafold
@@ -835,7 +830,7 @@ gget ref -w dna -d homo_sapiens
- Check PDB database first before running AlphaFold predictions
### Error Handling
- Database structures change; update gget regularly: `pip install --upgrade gget`
- Database structures change; update gget regularly: `uv pip install --upgrade gget`
- Process max ~1000 Ensembl IDs at once with gget info
- For large-scale analyses, implement rate limiting for API queries
- Use virtual environments to avoid dependency conflicts