Pathogenome

A suite of plugins to detect viral genomes and protein sequences from MAGs and contigs for antimicrobial-resistance.

Version
Built-in plugins

Installation Instructions

You can install this distribution with either conda or docker.

Table of Contents
  1. Using Conda
  2. 1. Installing Miniconda
  3. 2. Updating Miniconda
  4. 3. Install the base distribution’s conda environment
  5. 4. Test your install
  6. Using Docker
  7. 1. Install docker
  8. 2. Download base image
  9. 3. Test your install

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda

Miniconda provides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructions for downloading and installing Miniconda. It is important to follow all of the directions provided in the Miniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

   conda update conda

3. Install the base distribution’s conda environment

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-pathogenome-2024.10 to indicate what QIIME 2 release is installed (i.e. 2024.10).

Instructions
Linux / Windows WSL
macOS (Apple Silicon)
macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-pathogenome-2024.10
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/pathogenome:2024.10

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/pathogenome:2024.10 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/pathogenome:2024.10 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda

Miniconda provides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructions for downloading and installing Miniconda. It is important to follow all of the directions provided in the Miniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

   conda update conda

3. Install the base distribution’s conda environment

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-pathogenome-2024.10 to indicate what QIIME 2 release is installed (i.e. 2024.10).

Instructions
Linux / Windows WSL
macOS (Apple Silicon)
macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-pathogenome-2024.10
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/pathogenome:2024.10

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/pathogenome:2024.10 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/pathogenome:2024.10 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda

Miniconda provides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructions for downloading and installing Miniconda. It is important to follow all of the directions provided in the Miniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

   conda update conda

3. Install the base distribution’s conda environment

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-pathogenome-2024.10 to indicate what QIIME 2 release is installed (i.e. 2024.10).

Instructions
Linux / Windows WSL
macOS (Apple Silicon)
macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-pathogenome-2024.10
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/pathogenome:2024.10

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/pathogenome:2024.10 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/pathogenome:2024.10 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. Installing Miniconda

Miniconda provides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the Miniconda instructions for downloading and installing Miniconda. It is important to follow all of the directions provided in the Miniconda instructions, particularly ensuring that you run conda init at the end of the installation process (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands.

2. Updating Miniconda

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

   conda update conda

3. Install the base distribution’s conda environment

We highly recommend creating a new environment specifically for the QIIME 2 distribution and release being installed, as there are many required dependencies that you may not want added to an existing environment.

You can choose whatever name you’d like for the environment. In this example, we’ll name the environments qiime2-pathogenome-2024.10 to indicate what QIIME 2 release is installed (i.e. 2024.10).

Instructions
Linux / Windows WSL
macOS (Apple Silicon)
macOS (Intel)

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate qiime2-pathogenome-2024.10
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/pathogenome:2024.10

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/pathogenome:2024.10 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/pathogenome:2024.10 (-t).