I'm programming on Windows 7 and in one of my Python projects I need to call bedtools, which only works with Cygwin on Windows. I'm new to Cygwin, installed the default version + everything needed for bedtools and then used Cygwin to install bedtools by using make as described in the installation instructions.

$ tar -zxvf BEDTools.tar.gz
$ cd BEDTools-<version>
$ make

When I use the Cygwin terminal to call it manually like below, it works without problem and the output file contains the correct result.

bedtools_exe_path intersect -a gene_bed_file -b snp_bed_file -wa -wb > output_file

But when I use subprocess.call in my program it seems to use Windows cmd instead of Cygwin, which doesn't work.

arguments = [bedtools_exe_path, 'intersect', '-a', gene_bed_file, '-b',snp_bed_file, '-wa', '-wb', '>', output_file]
return_code = suprocess.call(arguments)

Results in no output file and a return code of 3221225781.

arguments = [bedtools_exe_path, 'intersect', '-a', gene_bed_file, '-b',snp_bed_file, '-wa', '-wb', '>', output_file]
return_code = suprocess.call(arguments, shell=True)

Results in an empty output file and a return code of 3221225781.

cygwin_bash_path = 'D:/Cygwin/bin/bash.exe'
arguments = [cygwin_bash_path, bedtools_exe_path, 'intersect', '-a', gene_bed_file, '-b',snp_bed_file, '-wa', '-wb', '>', output_file]
return_code = suprocess.call(arguments)

Results in no output file, a return code of 126 and

D:/BEDTools/bin/bedtools.exe: D:/BEDTools/bin/bedtools.exe: cannot execute binary file

arguments = [cygwin_bash_path, bedtools_exe_path, 'intersect', '-a', gene_bed_file, '-b',snp_bed_file, '-wa', '-wb', '>', output_file]
return_code = suprocess.call(arguments, shell=True)

Results in an empty output file, a return code of 126 and

D:/BEDTools/bin/bedtools.exe: D:/BEDTools/bin/bedtools.exe: cannot execute binary file

Any ideas how I can get it to work?

Imagine you want to run a Linux command from Windows. You could install Linux into a VM and run commands via ssh (Putty/plink on Windows):

#!/usr/bin/env python
import subprocesscmd = [r'C:\path\to\plink.exe', '-ssh', 'user@vm_host', '/path/to/bedtools']
with open('output', 'wb', 0) as file:subprocess.check_call(cmd, stdout=file)

Cygwin provides run command that allows to run commands directly:

cmd = [r'C:\cygwin\path\to\run.exe', '-p', '/path/to/', 'bedtools', '-wait', 'arg1', 'arg2']

Note: Python script is run from Windows in both cases. bedtools is Linux or Cygwin (non-Windows) command here and therefore you should provide POSIX paths.