Cutadapt requires a C compiler. On Windows you will be able to install the Python-only components of cutadapt, but the adapter alignment code is C, which is not provided as a pre-compiled binary. You'll need something like MinGW, which provides a C compiler, and then you can install Cython and cutadapt.
As some of us are locked in Windows environment, here is the procedure to get cutadapt up and running on Windows:
- get Python installed (I recommend Anaconda, it is pretty well equipped for scientific computing)
- search for and install Visual Studio C compiler for Python (e.g. VCForPython27.msi). If you have issues with installation from msi, follow the instructions here.
- start command prompt and type:
pip install cutadapt
This will install the most recent version of the cutadapt.
One additional hack that was needed (there is probably a more elegant and correct solution) was to copy the script: C:\Anaconda\Lib\site-packages\cutadapt\scripts\cutadapt.py (e.g. to working directory). Rename it (e.g. my_cutadapt.py) and call it with: