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Installation

Prerequisites

  • Python version has to be >= 3.10

Note

It is highly recommended to install blast2galaxy in an isolated environment created with an environment management tool like conda/mamba, pixi, virtualenv or similar.

Installation with pip

You can install blast2galaxy from PyPI.org using pip:

pip install blast2galaxy

After installation you can check if the blast2galaxy CLI was installed correctly by executing the following command on your shell:

blast2galaxy --help

Installation with mamba or conda

blast2galaxy is available as a Bioconda package.

Note

Please make sure you have added the channels bioconda and conda-forge to your mamba/conda settings. You can do this by executing the following commands:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

This will modify your ~/.condarc file.

You can install blast2galaxy the from the bioconda channel:

mamba install blast2galaxy

or

conda install blast2galaxy

After installation you can check if the blast2galaxy CLI was installed correctly by executing the following command on your shell:

blast2galaxy --help

Using Biocontainers image with Docker or Podman

blast2galaxy is available as a Biocontainers image.

Please replace <tag> in the commands listed below with an available version tag. All available version tags are listed here: https://quay.io/repository/biocontainers/blast2galaxy?tab=tags

Pull the image

Using Podman:

podman pull quay.io/biocontainers/blast2galaxy:<tag>

Using Docker:

docker pull quay.io/biocontainers/blast2galaxy:<tag>

Start a container

Using Podman:

$ podman run -it blast2galaxy:<tag>

Using Docker:

$ docker run -it blast2galaxy:<tag>

When the container is running you can check if everything works fine by executing the following command on the shell of the running container:

blast2galaxy --help

Using Apptainer (Singularity) image

Pull the image: 

$ apptainer pull blast2galaxy.sif https://depot.galaxyproject.org/singularity/blast2galaxy:<tag>

Start a container: 

$ apptainer shell blast2galaxy.sif

When the container is running you can check if everything works fine by executing the following command on the shell of the running container:

blast2galaxy --help