in reply to Re^4: Can't run Clustalw through Bioperl
in thread Can't run Clustalw through Bioperl

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.
  • Comment on Re^5: Can't run Clustalw through Bioperl

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Re^6: Can't run Clustalw through Bioperl
by dimitris852 (Acolyte) on Mar 14, 2016 at 04:37 UTC

    ---->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]

        The (x86) variant is where 32 bit applications live. The "plain" directory contains 64 bit apps. It's a pretty good bet that the OP's application is 32 bit.

        Premature optimization is the root of all job security
[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]

        yeap the file is clastalw2.exe and NOT clustalw.exe as written on perl error.I was cleary searching for wrong file.

        If I C:\> where clustalw2.exe I get eventually: C:\Program Files (x86)\ClustalW2\clustalw2.exeSo I can find the executable by command line. But

         'C:\Program Files (x86)\ClustalW2' is the same i use from the beggining, and even though I ve put ENV{CLUSTALDIR} on the script and add it to Windows Path variable i have this error..

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