diff --git a/README.md b/README.md index b30e719..107af96 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,9 @@ The development of this pipeline is part of the GPS Project ([Global Pneumococca # Table of contents - [Workflow](#workflow) - [Usage](#usage) - - [Requirement](#requirement) + - [Requirements](#requirements) + - [Software](#software) + - [Hardware](#hardware) - [Accepted Inputs](#accepted-inputs) - [Setup](#setup) - [Run](#run) @@ -47,12 +49,26 @@ The development of this pipeline is part of the GPS Project ([Global Pneumococca   # Usage -## Requirement -- A POSIX-compatible system (e.g. Linux, macOS, Windows with [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux)) with Bash 3.2 or later -- Java 11 or later (up to 21) ([OpenJDK](https://openjdk.org/)/[Oracle Java](https://www.oracle.com/java/)) -- [Docker](https://www.docker.com/) or [Singularity](https://sylabs.io/singularity/)/[Apptainer](https://apptainer.org/) - - For Linux, [Singularity](https://sylabs.io/singularity/)/[Apptainer](https://apptainer.org/) or [Docker Engine](https://docs.docker.com/engine/) is recommended over [Docker Desktop for Linux](https://docs.docker.com/desktop/). The latter is known to cause permission issues when running the pipeline on Linux. -- It is recommended to have at least 16GB of RAM and 50GB of free storage +## Requirements +### Software + - A POSIX-compatible operating system (e.g. Linux, macOS, Windows with [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux)) with Bash 3.2 or later + - [Installation guide for WSL on Windows](https://learn.microsoft.com/en-us/windows/wsl/install) by Microsoft + - Java 11 or later (up to 21) ([OpenJDK](https://openjdk.org/)/[Oracle Java](https://www.oracle.com/java/)) + - [Installation guide for OpenJDK](https://www.freecodecamp.org/news/install-openjdk-free-java-multi-os-guide/) by freeCodeCamp + - [Docker](https://www.docker.com/) or [Singularity](https://sylabs.io/singularity/)/[Apptainer](https://apptainer.org/) + - Installation guides: + - For Linux + > ℹ️ For Linux, [Docker Engine](https://docs.docker.com/engine/) or [Singularity](https://sylabs.io/singularity/)/[Apptainer](https://apptainer.org/) is recommended over [Docker Desktop](https://docs.docker.com/desktop/). The latter is known to cause permission issues when running the pipeline on Linux. + - [Docker Engine on Linux](https://docs.docker.com/engine/install/) by Docker + - [Apptainer on Linux](https://apptainer.org/docs/admin/main/installation.html) by Apptainer + - For macOS + - [Docker Desktop on macOS](https://docs.docker.com/desktop/install/mac-install/) by Docker + > ℹ️ After installation, you might need to [allow Docker to access more system resources](https://docs.docker.com/desktop/settings/mac/), especially CPU and Memory, to match the hardware requirement of the pipeline + - For Windows with WSL + - [Docker Desktop on Windows with WSL](https://docs.docker.com/desktop/wsl/) by Docker + +### Hardware +It is recommended to have at least 16GB of RAM and 50GB of free storage > ℹ️ Details on storage > - The pipeline core files use ~5MB > - All default databases use ~8GB in total