https://github.com/ncmbianchi/x86_bioinformatics_setup
A simple bash script to install bioinformatics tools that require x86_64 architecture.
https://github.com/ncmbianchi/x86_bioinformatics_setup
apple-silicon-support arm64 bioinformatics conda conda-environment homebrew pyenv pyenv-virtualenv python x86-64
Last synced: 6 months ago
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A simple bash script to install bioinformatics tools that require x86_64 architecture.
- Host: GitHub
- URL: https://github.com/ncmbianchi/x86_bioinformatics_setup
- Owner: NCMBianchi
- License: mit
- Created: 2025-04-15T07:30:52.000Z (6 months ago)
- Default Branch: main
- Last Pushed: 2025-04-15T09:25:47.000Z (6 months ago)
- Last Synced: 2025-04-15T23:15:48.516Z (6 months ago)
- Topics: apple-silicon-support, arm64, bioinformatics, conda, conda-environment, homebrew, pyenv, pyenv-virtualenv, python, x86-64
- Language: Shell
- Homepage:
- Size: 6.84 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
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README
# x86 Bioinformatics Setup
This script installs all dependencies necessary to manage different Python versions via Pyenv and Conda, in order to use bioinformatics tools that require x86_64 architecture and thus do not work on arm64 (Apple Silicon, M1-M3 processors).
## Features
- Allows to run packages such as [bowtie](https://anaconda.org/bioconda/bowtie) and [macs2](https://anaconda.org/bioconda/macs2) that are not –or not fully– supported in arm64.
- Installs the 2.2.2. version of [PyTorch](https://pytorch.org/get-started/previous-versions/) and its dependencies.
- Installs [R](https://www.r-project.org) to run scripts locally within hybrid pipelines, but not [Rstudio](https://posit.co/downloads/) which only recognises the default R version (check the [Rig](https://github.com/r-lib/rig) repository to manage different versions of R in Rstudio).
## Installation
Clone this repository, move into it and activate the scritp with:
```
chmod +x ./arm64_setup.sh
```
Then run it with:
```
./arm64_setup.sh
```
Installing it might take a while. It takes care also of installing [homebrew](https://brew.sh) if it's not already installed. I highly suggested using it to install any tool that is required even within virtual environments. This script assumes ZSH as the currently used shell, yet the `--fish` parameters allows to instead set up according to the [fish shell](https://fishshell.com).
## License
This project is licensed under the MIT License. Feel free to use and modify the code as per your needs.