# Installing Mimick

There are three ways you can install Mimick: conda, pixi, pip. Make note of the names of the code blocks, as they describe installation and usage variations.

# Install with conda

To install Mimick using conda (or miniconda, mamba, etc.) into an existing environment, it's as simple as:

you're already in the environment
$ conda install -c conda-forge bioconda::mimick

you're not in the environment
conda install -n env_name -c conda-forge bioconda::mimic

where env_name is the name of the existing conda environment you want to install Mimick into. Alternatively, you can create a new conda environment and install Mimick into it using one command:

global environment
conda create -n mimick -c bioconda -c conda-forge mimick

local environment
conda create -p path/to/workdir/mimick -c bioconda -c conda-forge mimick

# Using with conda

You'll need to activate the environment you installed Mimick into, then call it with:

run Mimick
mimick options... args...

# Updating with conda

If you wish to update Mimick, just replace word create/install in the commands above with update, e.g.:

you're already in the environment
conda update -c conda-forge bioconda::mimick

you're not in the environment
conda update -n env_name -c conda-forge bioconda::mimick

# Install with pixi

Pixi is a new ultra-fast Rust-based environment manager much like conda is. If you haven't tried it out, you ought to give it a shot. With it, you can install Mimick to be accessible in your PATH, i.e. a "global" installation:

global install
pixi global install -c conda-forge -c bioconda mimick

local install
pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add mimick

Make sure ~/.pixi/bin is in your PATH using export PATH=~/.pixi/bin:$PATH

# Using with pixi

If installed globally, this is very similar to the conda installation:

install globally
mimick options... args...

If you installed Mimick locally using Pixi, you can do one of two things:

activate the pixi shell in the directory you installed it into, then run mimick:

installed locally and activate environment
pixi shell
mimick options... args...

be in the directory you installed Mimick into and call it with pixi run mimick instead of just mimick:

installed locally and not activating environment
pixi run mimick options... args...

# Updating with pixi

Once again, slightly different depending on whether it was installed globally or locally:

installed globally
pixi global update mimick

installed locally
cd path/to/projectdir
pixi update mimick

# Install with pip

If neither conda nor pixi appeal to you, Mimick can be installed with pip too. To do that, you will need to first download the latest release (recommended) or clone the git repository:

download the latest release
# (replace x.x.x with the actual version #)
wget -O mimick.tar.gz https://github.com/pdimens/mimick/releases/download/x.x.x/mimick.x.x.x.tar.gz
tar -xvzf mimick.tar.gz

clone the repository
git clone https://github.com/pdimens/mimick.git

Then, you will need to enter the Mimick directory and do a local pip installation:

local pip installation
cd mimick
pip install .

# Using with pip

Just call mimick from the command line

call Mimick
mimick options... args...

# Updating with pip

You'll need to repeat the Install with pip process above.