DOC Update installation docs

1. Recommend pixi
2. Do not recommend fraggenescan

Author: luispedro

README.md

@@ -24,7 +24,8 @@ well as their benchmarking) are described in
 
 A tutorial of running SemiBin from scrath can be found here [SemiBin tutorial](https://github.com/BigDataBiology/SemiBin_tutorial_from_scratch).
 
-Installation:
+
+Installation with `conda`:
 
 ```bash
 conda create -n SemiBin
@@ -59,20 +60,29 @@ Please find more options and details below and [read the docs](https://semibin.r
 
 SemiBin runs (and is continuously tested) on Python 3.7-3.13
 
-### Bioconda
+### pixi
 
-The simplest mode is shown above.
-However, if you want to use SemiBin with GPU (which is faster if you have one available), you need to install PyTorch with GPU support:
+The current recommended way to install SemiBin with GPU-support is to use [pixi](https://pixi.sh/). Pixi will use the packages from conda-forge and bioconda to install SemiBin and its dependencies. See [the docs](https://semibin.readthedocs.io/en/latest/install/) for more details, but the basic idea is to create a `pixi.toml` file with the following content:
 
-```bash
-conda create -n SemiBin
-conda activate SemiBin
-conda install -c conda-forge -c bioconda semibin
-conda install -c pytorch -c nvidia pytorch pytorch-cuda=11.8
+```toml
+[project]
+authors = ["Luis Pedro Coelho <luis@luispedro.org>"]
+channels = ["conda-forge", "bioconda"]
+name = "semibin_install"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+semibin = ">=2.1.0,<3"
+pytorch-gpu = "*"
+
+[system-requirements]
+cuda = "12.0"
 ```
 
-_MacOS note_: **you can only install the CPU version of PyTorch in MacOS with `conda` and you need to install from source to take advantage of a GPU** (see [#72](https://github.com/BigDataBiology/SemiBin/issues/72)).
-For more information on how to install PyTorch, see [their documentation](https://pytorch.org/get-started/locally/).
+This will install SemiBin with GPU support, but it does require a CUDA-compatible GPU. Alternatively, you can install SemiBin in CPU-only mode by removing the `pytorch-gpu` and `cuda` lines.
 
 ### Source
 

docs/install.md

@@ -1,12 +1,60 @@
 # Install
 
-SemiBin can run on Python 3.7-3.12.
+SemiBin can run on Python 3.7-3.13.
+
+## Install with pixi
+
+The current recommended way to install SemiBin is to use [pixi](https://pixi.sh/). Pixi will use the packages from conda-forge and bioconda to install SemiBin and its dependencies.
+
+### CPU-only mode
+
+Create a `pixi.toml` file with the following content.
+
+```toml
+[project]
+authors = ["Luis Pedro Coelho <luis@luispedro.org>"]
+channels = ["conda-forge", "bioconda"]
+name = "semibin_install"
+platforms = ["linux-64", "osx-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+semibin = ">=2.1.0,<3"
+```
+
+Then, run `pixi install` in the same directory as the `pixi.toml` file to download and install SemiBin2.
+
+
+### With GPU support
+
+If you want to use SemiBin with GPU, you need to install Pytorch with GPU support as well. Starting with the example above, you need to add `pytorch-gpu` to the `dependencies` section and `cuda` to the `system-requirements` section.
+
+```toml
+[project]
+authors = ["Luis Pedro Coelho <luis@luispedro.org>"]
+channels = ["conda-forge", "bioconda"]
+name = "semibin_install"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+semibin = ">=2.1.0,<3"
+pytorch-gpu = "*"
+
+[system-requirements]
+cuda = "12.0"
+```
 
 ## Install from bioconda
 
-### Simple Mode
 
-The simplest way to install is to use [conda](https://conda.io/).
+Pixi is now the recommended way to install SemiBin. However, if you prefer to use conda, you can install SemiBin with it
+
+### Simple Mode
 
 ```bash
 conda create -n SemiBin
@@ -28,17 +76,14 @@ conda install pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch-lts
 ## Install from source
 
 You will need the following dependencies:
-- [MMseqs2](https://github.com/soedinglab/MMseqs2)
 - [Bedtools](http://bedtools.readthedocs.org/]), [Hmmer](http://hmmer.org/)
 - [Prodigal](https://github.com/hyattpd/Prodigal)
-- (optionally) [Fraggenescan](https://sourceforge.net/projects/fraggenescan/)
 
 
 You can obtain them from conda with the following commands
 
 ```bash
-conda install -c conda-forge -c bioconda mmseqs2=13.45111
-conda install -c bioconda bedtools hmmer fraggenescan samtools
+conda install -c bioconda bedtools hmmer samtools
 ```
 
 Then, installing should be a simple matter of running: