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Add instructions for configuring signalp6 to README.md

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Alex Morehead 2024-03-10 14:56:18 -05:00 committed by GitHub
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@ -42,15 +42,23 @@ pip3 install --no-cache-dir -r requirements.txt
python3 setup.py install python3 setup.py install
cd ../../ cd ../../
``` ```
4. Install input preparation dependencies 4. Configure signalp6 after downloading a licensed copy of it from https://services.healthtech.dtu.dk/services/SignalP-6.0/
```
# NOTE: (current) version 6.0h is used in this example, which was downloaded to the current working directory using `wget`
signalp6-register signalp-6.0h.fast.tar.gz
# NOTE: once registration is complete, one must rename the "distilled" model weights
mv $CONDA_PREFIX/lib/python3.10/site-packages/signalp/model_weights/distilled_model_signalp6.pt $CONDA_PREFIX/lib/python3.10/site-packages/signalp/model_weights/ensemble_model_signalp6.pt
```
5. Install input preparation dependencies
``` ```
bash install_dependencies.sh bash install_dependencies.sh
``` ```
5. Download the model weights. 6. Download the model weights.
``` ```
wget http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt wget http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt
``` ```
6. Download sequence databases for MSA and template generation. 7. Download sequence databases for MSA and template generation.
``` ```
# uniref30 [46G] # uniref30 [46G]
wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz