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Rich Mayne edited this page Feb 25, 2026 · 4 revisions

Installation from source

Linux

Prerequisites

We assume the user's system is set up with the following. See attached links for guidance if not.

  1. A Linux-like environment: tested on Ubuntu 22.04 and Windows Subsystems Linux (WSL2) Ubuntu 22.04.
  2. Conda (for managing packages). See https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html
  3. Python > 3.7 <= 3.12 (developed for 3.10), ideally installed specifically to a Conda environment made for running Castanet.
  4. Ensure your distribution packages are up to date. On Ubuntu and other Debian-based Linux: $ sudo apt update -y

Environment setup

Your hardware and software configurations will vary from ours: the following should be used as guidance only and is not a subsitute for technical expertise, especially when users opt to install this on institutional machines and/or HPC devices. Users should study the terminal output to check for the success of each stage. If in doubt, contact your system administrator.

  1. Create a new Conda environment: $ conda create --name castanet python==3.10
  2. Activate Conda environment $ conda activate castanet
  3. Install bioinformatics CLI dependencies $ bash install_deps.sh
  4. (Optional: alias the command to start a Castanet server; if doing on Mac, sub "bashrc" for "zshrc") $ echo "alias castanet='conda activate castanet && uvicorn app.api:app --reload --port 8001'" >> ~/.bashrc, then refresh your terminal with $ source ~/.bashrc.

Mac/OSX

The Linux guide can be followed as a guideline, with a few modifications. A different Conda channel will need to be added to your environment, and this will be specific to the OSX build you are running, i.e. Intel or Apple Silcon (i.e. osx-arm64); please refer to the Conda documentation. Alternatively, users may opt to install each dependency manually (listed in install_deps.sh), in which case their calls will need to be mapped to the correct terminal commands (e.g. trimmomatic will need to be callable from the terminal, using the command trimmomatic). Further, the installer script will need to be called with $ sh install_deps.sh, if bash is unavailable.

Windows

Windows users are strongly encouraged to install Windows Subsystems for Linux (WSL2), which is fully compatible (Link to Microsoft documentation).

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