Question: Cutadapt On Windows
0
gravatar for anandsprodigy
5.1 years ago by
anandsprodigy0 wrote:

Can anybody give me detailed procedure on cutadapt installation on windows? Because whenever i installed/ run cutadapt using python it is not working? Although there is comprehensive readme document.

windows • 4.0k views
ADD COMMENTlink modified 2.7 years ago by emmaggie10 • written 5.1 years ago by anandsprodigy0
3

most of the programs give an error message when something is wrong. "not working" does not give anybody a possibility to help you. Maybe its not in your PATH?

ADD REPLYlink written 5.1 years ago by Ido Tamir4.9k
2
gravatar for Matt Shirley
5.1 years ago by
Matt Shirley8.7k
Cambridge, MA
Matt Shirley8.7k wrote:

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.

ADD COMMENTlink written 5.1 years ago by Matt Shirley8.7k
1
gravatar for emmaggie
2.7 years ago by
emmaggie10
United States
emmaggie10 wrote:

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:

python my_cutadapt.py
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by emmaggie10
0
gravatar for Shahzad
3.1 years ago by
Shahzad10
Pakistan
Shahzad10 wrote:

Hi

Can we use Cygwin instead MinGW?

 

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Shahzad10

You should be able to use Cygwin.  Though I'd recommend switching to Linux, or else using BBDuk, which can runs in Windows or Linux without needing recompilation or an emulator.

ADD REPLYlink written 3.1 years ago by Brian Bushnell16k
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