Installation

Because Cutadapt development happens on Linux, this is the best supported platform, but it should also run on macOS and Windows.

Installation with Conda

Cutadapt is available as a Conda package from the Bioconda channel.

  1. Install Conda. For example, by installing miniforge.

  2. Configure the Bioconda channel by following the Bioconda setup instructions. In short:

    conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

    (The Bioconda instructions mention the defaults channel, but it is not needed.)

  3. Install Cutadapt into a new Conda environment:

    conda create -n cutadapt cutadapt

    The first cutadapt in this command is the name of the Conda environment. You can choose a different name.

    If you are on macOS and your machine uses an M1/M2 processor (Apple Silicon), you may need to run this command instead:

    CONDA_SUBDIR=osx-64 conda create -n cutadapt cutadapt

    (If you have problems, see this issue for troubleshooting.)

  4. Activate the Conda environment. This needs to be done every time you open a new shell in order to be able to use Cutadapt:

    conda activate cutadapt

  5. Finally, check whether the installation was successful:

    cutadapt --version

    This should show the Cutadapt version number.

Installation with pipx

This works on Ubuntu 20.04 and later:

sudo apt install pipx python3-venv
pipx install cutadapt
cutadapt --version

Installation with pip

Ensure you have virtualenv installed. On Ubuntu/Debian:

sudo apt install python3-virtualenv

Create a new virtual environment and install Cutadapt into it:

virtualenv cutadapt-venv
cutadapt-venv/bin/pip --upgrade pip
cutadapt-venv/bin/pip install cutadapt

Cutadapt is now available as cutadapt-venv/bin/cutadapt:

cutadapt-venv/bin/cutadapt --version

Optionally, you can activate the virtual environment, which allows you to just type cutadapt without the full path:

source cutadapt-venv/bin/activate
cutadapt --version

Activation must be re-done whenever you open a new shell/terminal window.

Installation on Debian/Ubuntu

Cutadapt is also included in Debian-based Linux distributions, such as Ubuntu. Simply use your favorite package manager to install Cutadapt. On the command-line, this should work

sudo apt install cutadapt

or possibly

sudo apt install python3-cutadapt

Please be aware that distribution packages are very likely to be outdated. If you encounter unexpected behavior or need newer features, please use one of the other installation methods to get an up-to-date version before reporting bugs.

Installation on Windows

For some releases of Cutadapt, a single-file executable (cutadapt.exe) is made available on the GitHub releases page. Try that first, and if it does not work for you, please report the issue.

To install Cutadapt manually, keep reading.

There is no Bioconda package for Windows because Bioconda does not produce Windows packages. To install Cutadapt, you can use pip, but because Cutadapt contains components that need to be compiled, you also need to install a compiler.

  1. Download a recent version (at least 3.7) of Python for Windows from <https://www.python.org/> and install it.

  2. Download and install “Build Tools for Visual Studio 2019” from <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>. (There are many similarly named downloads on that page, ensure you get the right one.)

    During installation, when the dialog about which components to install pops up, ensure that “C++ Build tools” is ticked. The download is quite big and can take a long time.

  3. Open the command line (cmd.exe) and run py -m pip install cutadapt.

  4. Test whether it worked by running py -m cutadapt --version. You should see the version number of Cutadapt.

When running Cutadapt this way, you will need to remember to write py -m cutadapt instead of just cutadapt.

FreeBSD ports and pkgsrc

Cutadapt can be installed via the FreeBSD ports system. To install from a binary package, run:

pkg install py39-cutadapt

The p39 will change from time to time (py310, py311 etc.). Alternatively, peruse the FreeBSD ports documentation to install from source, which may result in better optimized binaries.

To install a binary package via the pkgsrc system (for example on NetBSD), run

pkgin install py311-cutadapt

The pkgsrc system also allows installation from source on any POSIX platform (including macOS), see the https://pkgsrc.org/.

Shared installation (on a cluster)

If you have a larger installation and want to provide Cutadapt as a module that can be loaded and unloaded (with the Lmod system, for example), we recommend that you create a virtual environment and ‘pip install’ Cutadapt into it. These instructions work on a SLURM cluster that uses the Lmod system (replace 3.1 with the actual version you want to use):

BASE=/software/cutadapt-3.1
virtualenv $BASE/venv
$BASE/venv/bin/pip install cutadapt==3.1
mkdir $BASE/bin
cd $BASE/bin
ln -s ../venv/bin/cutadapt

Then add the directory $BASE/bin/ to the $PATH when a user loads the module, somewhat like this (this is for the Lmod system):

conflict("cutadapt")
whatis("adapter trimming tool")
prepend_path("PATH", "/software/cutadapt-3.1/bin")

Make sure that you do not add $BASE/venv/bin/ to the $PATH! Otherwise, a user trying to run python who also has the cutadapt module loaded would get the python from the virtual environment, which leads to confusing error messages. The $BASE/bin/ directory only contains the cutadapt script and nothing else, avoiding this problem.

Please note that there is no need to “activate” virtual environments.

Installing the development version

We recommend that you install Cutadapt into a so-called virtual environment if you decide to use the development version. The virtual environment is a single directory that contains everything needed to run the software. Nothing else on your system is changed, so you can uninstall this particular version of Cutadapt by just removing the directory with the virtual environment.

The following instructions work on Linux using Python 3. Make sure you have installed the python3-dev and build-essential packages on Ubuntu.

First, choose where you want to place the directory with the virtual environment and what you want to call it. Let us assume you chose the path ~/cutadapt-venv. Then use these commands for the installation:

python3 -m venv ~/cutadapt-venv
~/cutadapt-venv/bin/python3 -m pip install --upgrade pip
~/cutadapt-venv/bin/pip install git+https://github.com/marcelm/cutadapt.git

To run Cutadapt and see the version number, type

~/cutadapt-venv/bin/cutadapt --version

The reported version number will be something like 2.2.dev5+gf564208. This means that you are now running the version of Cutadapt that will become 2.2, and that it contains 5 changes (commits) since the previous release (2.1 in this case).