Installation

There are several ways to install Galah

Install from Bioconda via Pixi

Create pixi.toml file:

[workspace]
channels = ["conda-forge", "bioconda"]
name = "galah"
platforms = ["linux-64"]

[dependencies]
galah = "*"

Create pixi environment.

pixi install

# Either run within your current environment
pixi run galah -h
# Or enter the environment
pixi shell

One can see details of the galah recipe.

Galah can also be used indirectly through CoverM via its cluster subcommand, which is also available on bioconda.

Install from Bioconda via Conda

Install latest release via conda (or mamba).

conda create -n galah -c bioconda -c conda-forge galah

# Activate the environment
conda activate galah

Pre-compiled binary

Galah can be installed by downloading statically compiled binaries, available on the releases page.

Third party dependencies listed below are required for this method.

Compiling from source

Galah can also be installed from source, using the cargo build system after installing Rust.

cargo install galah

Third party dependencies listed below are required for this method.

Development

To run an unreleased version of Galah, after installing Rust:

git clone https://github.com/wwood/galah
cd galah
pixi run cargo run -- cluster ...etc...

Dependencies

Some usages of Galah require third party tools, which must be installed separately:

• skani v0.2.2 https://github.com/bluenote-1577/skani
• FastANI v1.34 https://github.com/ParBLiSS/FastANI
• Barrnap v0.9 https://github.com/tseemann/barrnap
• tRNAscan-SE v2.0.12 https://github.com/UCSC-LoweLab/tRNAscan-SE
• CheckM2 v1.1.0 https://github.com/chklovski/CheckM2

These tools can be installed via pixi, using the pixi.toml file within the github repository.

pixi install

Note that CheckM2 requires a database to be set using the environment variable CHECKM2DB or the argument --checkm2-db. See https://github.com/chklovski/CheckM2 for details.