Installation¶
Quickstart¶
The easiest way to install cutadapt is to use pip
on the command line:
pip install --user --upgrade cutadapt
This will download the software from PyPI (the Python packaging
index), and
install the cutadapt binary into $HOME/.local/bin
. If an old version of
cutadapt exists on your system, the --upgrade
parameter is required in order
to install a newer version. You can then run the program like this:
~/.local/bin/cutadapt --help
If you want to avoid typing the full path, add the directory
$HOME/.local/bin
to your $PATH
environment variable.
Installation with conda¶
Alternatively, cutadapt is also available as a conda package from the bioconda channel. If you do not have conda, install miniconda first. Then install cutadapt like this:
conda install -c bioconda cutadapt
If neither pip nor conda installation works, keep reading.
Dependencies¶
Cutadapt requires this software to be installed:
- One of Python 2.6, 2.7, 3.3, 3.4 or 3.5. Python 2.7 is a bit faster than the other versions.
- A C compiler.
Under Ubuntu, you may need to install the packages build-essential
and
python-dev
(or python3-dev
).
Installation¶
If you have already downloaded and unpacked the .tar.gz
file, then
installation is done like this (replace “python” with “python3” to
install the Python 3 version):
python setup.py install --user
If you get an error message:
error: command 'gcc' failed with exit status 1
Then check the entire error message. If it says something about a missing Python.h
file, then you need to install the Python development packages. The
appropriate package is called python-dev
in Ubuntu (or python3-dev
for Python 3).
System-wide installation (root required)¶
If you have root access, then you can install cutadapt system-wide by running:
sudo pip install cutadapt
This installs cutadapt into /usr/local/bin.
If you want to upgrade from an older version, use this command instead:
sudo pip install --upgrade cutadapt
Uninstalling¶
Type
pip uninstall cutadapt
and confirm with y
to remove the package. Under some circumstances, multiple
versions may be installed at the same time. Repeat the above command until you
get an error message in order to make sure that all versions are removed.