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.
If the above does not work, keep reading.
Dependencies¶
Cutadapt requires this software to be installed:
One of Python 2.6, 2.7, 3.3 or 3.4. 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
.
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¶
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
Use without installation¶
Build the C extension module (you can try to skip this step -- a compiled version of the module for Linux x86_64 is already included):
python setup.py build_ext -i
Then simply run the script from where it is, similar to this:
bin/cutadapt --help
If you get any errors, first try to explicitly request a specific Python version by running cutadapt like this:
python2.7 bin/cutadapt --help