# 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

Then, run the install script provided by Mimick itself, which will install the internally-bundled MimickLinkedReads.jl Julia package.

# activate environment with mimick...
install_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

Because of the Julia package backend, you will need to reinstall the Julia package:

# activate environment with mimick...
install_mimick

# Install with pixi

Julia does not install correctly when using Pixi. Do not use this method.

See here for more information

# 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 .

Then, run the install script provided by Mimick itself, which will install the internally-bundled MimickLinkedReads.jl Julia package.

# activate environment with mimick...
install_mimick

# 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.