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I have an web application hosted with Django-gUnicorn-Nginx. The web app is working mostly fine and is accessible except for one functionality.

Recently, I added pybedtools, a python wrapper package for bedtools. I have the binary executables of bedtools in the PATH variable. However, the server is unable to access this executable.

The error just reports intersectBed does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method

I have tested/reinstalled the latest versions locally and it works, but not in the server.

Any ideas? Thanks in advance.

deman23
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1 Answers1

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Good old print statements came to rescue!

The path variable passed on to the server instance somehow had only the defaults /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin.

I couldn't manage to export the location where bedtools is installed to the PATH. So I simply created a symlink of bedtools executable in my /usr/local/bin

Thanks for the suggestions Gerard.

deman23
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