in reply to Re^3: Can't run Clustalw through Bioperl
in thread Can't run Clustalw through Bioperl

--->INFO: Could not find files for the given pattern(s).

But i can see it. Its already installed on my computer and the Clusterw.exe is on this specific path. really confused...

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Re^5: Can't run Clustalw through Bioperl
by 1nickt (Canon) on Mar 14, 2016 at 04:00 UTC

    If you change into the folder where the file lives, can you execute it from the command line? If so, what does it tell you?

    The way forward always starts with a minimal test.
[reply]

      ---->System couldn't file Clustalw

      But I can double click on it and use it. Please excuse me for all this confusion, but it makes no sense to me.

[reply]
        $ENV{CLUSTALDIR} = 'C:\Program Files (x86)\ClustalW2';

        Please look very carefully at the path. On my current machine, I have both /Program Files (x86)/ and just /Program Files/ directories. Almost all my Program Files are in the "plain" directory. Just one program lives in /Program Files (x86)/.

        I can't say for sure whether this will help or not, but it is an anomaly that I noticed on this particular machine.

[reply]

        --->System couldn't file Clustalw

        Isn't the file supposed to be called clustalw.exe? Does the error message really mention a file with a capital letter in the name?

        I fear you have some basic file path/permission problem, with which I could scarcely help from afar, even if I knew Windows.

        The way forward always starts with a minimal test.
[reply]
[d/l]

        What is the name of the file you double click on. Is it clustalw2.exe ?

        poj
[reply]
[d/l]

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