Question: Cutadapt installation for Windows 10
gravatar for andy.hudson
21 months ago by
andy.hudson0 wrote:

Good day,

I am trying to install Cutadapt in Windows 10 but I am have some problems with this. I have been following the installation instructions on:, however with no success. As per the instructions, I have installed pip and the Microsoft Visual C++ 2017 BuildTools (the link on the Cutadapt installation page is broken for Microsoft Visual C++ Compiler for Python 2.7). When I try to install Cutadapt via pip, I get the following error:

c:\users\andy\appdata\local\programs\python\python36\include\pyconfig.h(59): fatal error C1083: Cannot open include file: 'io.h': No such file or directory error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\VC\Tools\MSVC\14.14.26428\bin\HostX86\x64\cl.exe' failed with exit status 2

I also went and retrieved the missing file and this revealed some other missing files (which I also retrieved). Ultimately, I still get the following error upon trying to install Cutadapt via pip:

c:\users\andy\appdata\local\programs\python\python36\include\io.h(26): warning C4068: unknown pragma
c:\users\andy\appdata\local\programs\python\python36\include\_mingw.h(32): warning C4068: unknown pragma
c:\users\andy\appdata\local\programs\python\python36\include\sdkddkver.h(26): warning C4068: unknown pragma
c:\users\andy\appdata\local\programs\python\python36\include\_mingw.h(49): fatal error C1189: #error:  ERROR: You must use a GNU Compiler.
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\BuildTools\\VC\\Tools\\MSVC\\14.14.26428\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2

Has anyone else had these problems and/or successfully installed Cutadapt in Windows 10? Any suggestions/advise would be really appreciated!


Andy Hudson

cutadapt windows 10 rna-seq • 1.4k views
ADD COMMENTlink modified 21 months ago by WouterDeCoster43k • written 21 months ago by andy.hudson0

Can you use the linux subsystem for windows 10? That would probably make this installation less painful.

In addition, please select appropriate tags for your question. In this case 'cutadapt' and 'windows 10' should have been there, so I've added them. As such experts can find your question more easily. Take this into account when asking more questions.

ADD REPLYlink written 21 months ago by WouterDeCoster43k

or install conda/miniconda on windows. Let conda handle installations @OP

ADD REPLYlink modified 21 months ago • written 21 months ago by cpad011212k

Thanks to you both for the suggestions. I will see if conda gives me more success or else use a Linux os.

Sorry about the missed tags in my post. I just saw the common tags in the dropdown when writing the post and figured I could only pick from these.

Thanks again!!

ADD REPLYlink written 21 months ago by andy.hudson0
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