Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-11-18

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All times shown according to UTC.

Time Nick Message
00:25 Isorropia I'm having a problem with using clustalw through bioperl. I'm including the Bio::Tools::Run::Alignment::Clustalw module in my script, and I have a clustalw2 executable in the same directory I'm running my scripts from, but in a sample script I'm getting the error message "'align' is not recognised as an internal or external command, operable program or batch file." I've been looking at
00:25 Isorropia http://doc.bioperl.org/bioperl-run/B‚Äčio/Tools/Run/Alignment/Clustalw.html to try and get it to work but I haven't had success with it so far.
00:33 leont Is the current directory in your $PATH?
00:34 Isorropia I don't think I have a path set, how would I go about doing it?
00:35 Isorropia also for what it's worth I'm using windows vista
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06:29 Isorropia Ok, so I've still got the same problem from earlier - trying to run a perlscript interfacing with clustalw2. I'm using windows, so I've just associated .pl with perl, not sure if that messes with the path to perl or not. The clustalw2 executable is in the same directory I'm running the scripts from, and from the setup page I've included the line "BEGIN { $ENV{CLUSTALDIR} = '/home/Hayden/binf
06:29 Isorropia /clustalw2/' }" near the beginning of my script
06:30 Isorropia when I run it I get 'align' is not recognised as an internal or external operable program or batch file
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