diff --git a/README.md b/README.md index 97d7ba8..e6694cc 100644 --- a/README.md +++ b/README.md @@ -30,12 +30,13 @@ unicore -v ``` ### GPU acceleration with Foldseek-ProstT5 -Foldseek provides a GPU-compatible static binary for ProstT5 prediction (requires Linux with AVX2 support, `glibc` ≥2.17, and `nvidia-driver` ≥525.60.13)
-To use it, please install it by running the following command: -``` -wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz; tar xvfz foldseek-linux-gpu.tar.gz; export PATH=$(pwd)/foldseek/bin/:$PATH -``` -Then, add `--gpu` options to either `easy-core` or `createdb` module to use Foldseek implementation of ProstT5-GPU: +Foldseek features GPU-acceleration for ProstT5 prediction under following requirements: + * Turing or newer NVIDIA GPU + * `foldseek` ≥10 + * `glibc` ≥2.17 + * `nvidia-driver` ≥525.60.13 + +Apply `--gpu` option to either `easy-core` or `createdb` module to use it, e.g. ``` unicore easy-core --gpu ``` @@ -52,7 +53,7 @@ unzip unicore_example.zip If you cloned the repository, you can find the example dataset in the `example/data` folder. ### Download ProstT5 weights -You need to first download the ProstT5 weights to run the `createdb` module. +You can preliminarily download the ProstT5 weights required to run the `createdb` module. ``` foldseek databases ProstT5 weights tmp ``` @@ -133,8 +134,6 @@ This module runs much faster with GPU. Please install `cuda` for GPU acceleratio To run the module, please use the following command: ``` -// Download ProstT5 weights as below if you haven't already -// foldseek databases ProstT5 /path/to/prostt5/weights tmp unicore createdb data db/proteome_db /path/to/prostt5/weights ``` This will create a Foldseek database in the `db` folder. @@ -211,7 +210,7 @@ unicore gene-tree --realign --threshold 30 --name /path/to/hashed/gene/names tre ## Build from Source ### Minimum requirements * [Cargo](https://www.rust-lang.org/tools/install) (Rust) -* [Foldseek](https://foldseek.com) (version ≥ 9) +* [Foldseek](https://foldseek.com) (version ≥ 10) * [Foldmason](https://foldmason.foldseek.com) * [IQ-TREE](http://www.iqtree.org/) ### Optional requirements @@ -232,5 +231,5 @@ With these tools installed, you can install and run `unicore` by: git clone https://github.com/steineggerlab/unicore.git cd unicore cargo build --release -bin/unicore help +bin/unicore -v ```