General Terminal Info and Help Links for Novices

The following are links to helpful webpages based on your operating system. These contain basic starter info for those who have no previous experience with terminals or commands.

Operating System

Linux

Here, you can find a tutorial covering the basics of the Linux command line, using Ubuntu.

Other informative pages can be found here and here.

Mac

Click here for terminal basics.

Windows - MUST use Ubuntu

Click here for the Ubuntu download page, or download in the Microsoft store.

Here, you can find a tutorial covering the basics of the Linux command line, using Ubuntu.

Installation

Installing MetaCerberus 1.3 manually due to Mamba/Conda issue (Newest Version)

Important

You still need to have Mamba and Conda installed. You cannot just use Mamba/Conda directly for the new version, currently. Click here for Conda download instructions. For each command given, enter the first line of the command, then press ENTER. Once the operation completes, the terminal prompt will reappear (blinking vertical line where you type). Proceed to the next line of the given command, press ENTER. Continue as such, line by line, until the entire given command has been entered.

In the command line, type:

git clone https://github.com/raw-lab/MetaCerberus.git
cd metacerberus
bash install_metacerberus.sh
conda activate MetaCerberus-1.3.0
metacerberus.py --download

Installing MetaCerberus 1.2.1 and below (due to current Mamba and Conda errors)

Note

We will update this as soon as Mamba/Conda corrects this error.

Option 1) Mamba

Note

Make sure to install Mamba in your base Conda environment unless you have OSX with ARM architecture (M1/M2 Macs). Follow the OSX-ARM instructions below if you have a Mac with ARM architecture.

Mamba install from bioconda with all dependencies:

Linux/OSX-64

Install Mamba using Conda

In command line, type:

conda install mamba

Install MetaCerberus with Mamba

In command line, type:

mamba create -n metacerberus -c bioconda -c conda-forge metacerberus
conda activate metacerberus
metacerberus.py --setup

OSX-ARM (M1/M2) [if using a Mac with ARM architecture]

Set up Conda environment

In command line, type:

conda create -y -n metacerberus
conda activate metacerberus
conda config --env --set subdir osx-64

Install Mamba, Python, and Pydantic inside the environment

In command line, type:

conda install -y -c conda-forge mamba python=3.10 "pydantic<2"

Install MetaCerberus with Mamba

In command line, type:

mamba install -y -c bioconda -c conda-forge metacerberus
metacerberus.py --setup

Note

Mamba is the fastest installer. Anaconda or miniconda can be slow. Also, install Mamba from Conda, NOT from pip. The Mamba from pip doesn’t work for install.

Option 2) Anaconda - Linux/OSX-64 Only

Anaconda install from bioconda with all dependencies:

In command line, type:

conda create -n metacerberus -c conda-forge -c bioconda metacerberus -y
conda activate metacerberus
metacerberus.py --setup