bowtie-2 build error

Question

[NGS-Newbie]

Hi All

I am trying to build bowtie index, on Windows 10 using CygWin. Getting the following error when I run - bowtie2-build myfile.fa index_file

Traceback (most recent call last):
  File "/usr/local/bin/bowtie2-build", line 95, in <module>
    main()
  File "/usr/local/bin/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 8] Exec format error

Any ideas on how to fix it?

Thanks so much!

UPDATE: I tried using the prebuilt version of Bowtie2 as well. I get the same error.

[h.mon]

Try running with --debug and / or --verbose. And use linux.

[NGS-Newbie]

Thanks, h.mon!

I am trying to figure out if I could use it at all on windows.

[WouterDeCoster]

Unless there really is a reason that you are not allowed to use Linux you are only making it more painful for yourself.

[NGS-Newbie]

Thank you WouterDeCoster!

Would there be any workarounds? MinGW (as I understand this is a minimalist version of CygWin) or Ubuntu?

[h.mon]

Ubuntu or any other linux distribution. Ubuntu is generally easy to install and use, so it is a commonly used distribution. I personally prefer Xubuntu over Ubuntu. But really, any distribution a friend of yours use is fine, this way, you will have "local support".

[WouterDeCoster]

I think the most support online is available for Ubuntu, the most common "Linux starter" system (I also use it). The flavor of Linux doesn't really matter.

[GenoMax]

Use the bash shell built into Win10. If you don't want to use a real unix distro or a VM.

[WouterDeCoster]

I've never tried bash on Windows10 (or windows10 at all), can you do everything in Win10 Bash now? Because if so I might have to stop windows bashing on biostars (pun intended).

[GenoMax]

With exception of fastq-dump everything else that does not need a GUI works in bash shell on Win10 (ref @Istvan, Win10 bash setup is covered in Biostar handbook). A few programs I tested have worked fine.