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Download and Installation

Overview

There are two different ways to use Metalign: the Bioconda package, or the locally-installed repository. The Bioconda package is highly recommended because setting up the libraries in the repository can be tricky, especially if you do not have root privileges. Also please note that the locally-install Metalign repository has only been tested on Linux systems.

With that being said, for either method, you first have to install the repository and download the database:

git clone https://github.com/nlapier2/Metalign.git
cd Metalign
./setup_data.sh

The last step will take a few hours. The exact time will depend on your internet connection.

The instructions below are specific to whether you are using Bioconda or the local repo (you can do both if you want).

Bioconda version

Simply run:

conda install -c conda-forge -c bioconda Metalign

Local repository version

Bioconda is the preferred installation method. However, if you cannot (or do not want to) use bioconda, you can simply manually install minimap2, KMC3, and CMash in the Metalign repository directory using instructions from their respective repositories:

Minimap2: https://github.com/lh3/minimap2/

KMC: https://github.com/refresh-bio/KMC

CMash: https://github.com/dkoslicki/CMash

This should look something like this:

git clone https://github.com/lh3/minimap2.git && cd minimap2 && make && cd ..
git clone https://github.com/refresh-bio/KMC.git  && cd KMC && make && cd ..
git clone https://github.com/dkoslicki/CMash.git && cd CMash && pip install --user -r requirements.txt && cd ..

*** Note: previously, we had a docker version of the package that was mentioned here. We no longer support the docker version, because the bioconda version is simpler to work with and due to docker's issues with running on clusters. However, the docker package is still available for legacy versions. ***