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:
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 build-essential and python-dev.
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).
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