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
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:
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.
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
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
file, then you need to install the Python development packages. The
appropriate package is called
python-dev in Ubuntu (or
for Python 3).
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:
If you get any errors, first try to explicitly request a specific Python version by running cutadapt like this:
python2.7 bin/cutadapt --help