[Bioperl-l] Solved: bioperl / emboss on windows

yi wang wangyi2412 at gmail.com
Tue May 5 03:32:42 EDT 2009

Thank you very much!

How big a mistake I have made!

I did not even got the emboss actually, but I thought the
bioperl,bioperl-run was enough, because the installed emboss.pm made me
think so. Now, it's clear the bioperl and bioperl-run are just base for
calling bio-perl module and external programs like emboss, but itself does
not contain such things. Emboss.pm is just a handle for calling that emboss
module. How foolish I was!

Thank you for your patient and detailed answer very much!

Best Wishes!

2009/5/5 <uludag at ebi.ac.uk>

> > I found beside mswin supporting, there is another problem:
> > *open(WOSSOUT, "wossname -auto |")
> > is not successful*, so the WOSSOUT is got empty, and the following while
> > loop does not executed, in which important data is set.
> As Scott wrote yesterday you can double check whether EMBOSS programs are
> included in your PATH environment variable. Installing mEMBOSS (version of
> EMBOSS for Windows) from EMBOSS ftp site should automatically update PATH
> environment variable (otherwise you should update it manually, Control
> Panel->System->Advanced->Environment Variables).
>  ftp://emboss.open-bio.org/pub/EMBOSS/windows/
> to check whether your PATH environment variable has successfully been
> updated you can call 'wossname -auto' command from Windows Command Prompt,
> it should return names of EMBOSS programs with their short descriptions.
> Regards,
> Mahmut


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