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Installation Guide

This guide explains how to set up Nanometa Live on your computer. For the smoothest installation, we suggest using Mambaforge.

Option 1: Install with Conda/Mamba (Recommended)

  1. Create a New Environment:

    To install Nanometa Live, first make a new environment in either Conda or Mamba. Run the following command in your terminal:

    mamba create --name nanometa_live_env nanometa-live

    This command creates an isolated space ('nanometa_live_env') for running Nanometa Live.

  2. Activate the Environment:

    Once the environment is ready, you need to switch to it. Do this with the following command:

    mamba activate nanometa_live_env

    You'll know you're in the right environment when you see 'nanometa_live_env' in your command prompt.

Option 2: Install with Docker

Using Docker, you can run Nanometa Live in a container, which is a great way to ensure it works consistently across different computers.

  1. Install Docker:

    If Docker is not already installed on your system, download and install it from the official Docker website. Follow the installation instructions for your specific operating system.

  2. Pull the Nanometa Live Docker image:

    To get the Nanometa Live image, use this command:

    docker pull quay.io/biocontainers/nanometa-live:0.4.3--pyhdfd78af_0

    This downloads the specific Nanometa Live image for Docker. Make sure to download the latest version.

  3. Start Nanometa Live in a Docker container:

    Start an interactive session in Docker container using:

    DATADIR=/path/to/host/data

docker run -it -v $DATADIR:$DATADIR -p 8050:8050 quay.io/biocontainers/nanometa-live:0.4.3--pyhdfd78af_0 /bin/bash

    Replace /path/to/host/data with your data folder path. The -v flag links your local data folder to the Docker container. The -p flag allows you to use Nanometa Live's web interface from your browser.

    After starting the Docker container, check if Nanometa Live is running:

    nanometa-live --version

  4. Learn More About Docker:

    FFor advanced Docker features, like setting environment variables or running in detached mode, see the Docker documentation.

Option 3: Install with Singularity

Nanometa Live can also be used through Singularity, a program that allows you to create and use containers. This method is especially useful if you can't or don't want to use Docker. It's a great choice for those who prefer using ready-made containers from Biocontainers.

  1. Check if Singularity is Installed:

    First, make sure you have Singularity on your computer. You can check by typing this command:

    singularity --version

    If Singularity is not installed, follow the installation guide on the official Singularity website.

  2. Pull Nanometa Live Container:

    Get the Nanometa Live container from Biocontainers using this command:

    DATADIR=/path/to/host/data

singularity  shell --nohttps --bind $DATADIR:$DATADIR docker://quay.io/biocontainers/nanometa-live:0.4.3--pyhdfd78af_0

    Replace /path/to/host/data with the path to your data. This command downloads the container with Nanometa Live.

  3. Start Nanometa Live in Singularity:

    Once you have the container, you can start Nanometa Live by running:

    nanometa-live --version

    This command opens Nanometa Live inside the Singularity container.

  4. Learn More About Singularity:

    If you want to customize how you use Singularity, check out the Singularity user guide.

Option 4: Install from source code

  1. Get the Source Code:

    Start by downloading the Nanometa Live code from GitHub:

    git clone https://github.com/FOI-Bioinformatics/nanometa_live

    This command copies the entire Nanometa Live project to your computer.

  2. Go to the Project Folder:

    Next, change to the directory where you downloaded the project. It should have a file called nanometa_live_env.yml.

    cd nanometa_live

  3. Set Up the Environment:

    Run the following command to create a new environment based on the nanometa_live_env.yml file:

    mamba env create -f nanometa_live_env.yml

  4. Activate the Environment:

    Activate the newly created environment:

    mamba activate nanometa_live_env

    You're now working in the environment specifically configured for Nanometa Live.

  5. Install the Program:

    While in the directory that contains the setup.py file, execute the following command to install the program:

    pip install .

    This command installs Nanometa Live on your system.