From 91707e6518c60752f99779e3c6dd6ee246471f59 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Tue, 5 Mar 2024 10:29:47 +1030 Subject: [PATCH] minor docs changes --- README.md | 6 +++--- docs/tutorial.md | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d733d94..3bac365 100644 --- a/README.md +++ b/README.md @@ -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` @@ -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 diff --git a/docs/tutorial.md b/docs/tutorial.md index 13bb887..ad903e3 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -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