8000 minor docs changes by gbouras13 · Pull Request #23 · gbouras13/phold · GitHub
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minor docs changes #23

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Mar 5, 2024
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minor docs changes #23

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6 changes: 3 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ phold install
* If you are running `phold` on a local work statio with GPU available, using `phold run` is recommended. It runs both `phold predict` and `phold compare`

```
phold run -i tests/test_data/pharokka.gbk -o test_output_phold -t 8
phold run -i tests/test_data/NC_043029.gbk -o test_output_phold -t 8
```

* If you do not have a GPU available, add `--cpu`
Expand All @@ -77,13 +77,13 @@ phold run -i tests/test_data/pharokka.gbk -o test_output_phold -t 8
1. Predict the 3Di sequences with ProstT5 using `phold predict`. This is massively accelerated if a GPU available.

```
phold predict -i tests/test_data/pharokka.gbk -o test_predictions
phold predict -i tests/test_data/NC_043029.gbk -o test_predictions
```

2. Compare the the 3Di sequences to the `phold` structure database with Foldseek using `phold compare`. This does not utilise a GPU.

```
phold compare -i tests/test_data/pharokka.gbk --predictions_dir test_predictions -o test_output_phold -t 8
phold compare -i tests/test_data/NC_043029.gbk --predictions_dir test_predictions -o test_output_phold -t 8
```

# Output
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3 changes: 2 additions & 1 deletion docs/tutorial.md
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Expand Up @@ -30,9 +30,10 @@ conda deactivate
## Step 3 Installing `phold`

* To install phold from source, replace the pip step with `pip install -e .`
* `phold` should work with Python v3.8-3.11. The below uses 3.11

```bash
mamba create -n pholdENV foldseek pip
mamba create -n pholdENV foldseek pip python=3.11
conda activate pholdENV
pip install phold
phold install
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