Re^8: Can't run Clustalw through Bioperl

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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Re^9: Can't run Clustalw through Bioperl by poj (Abbot) on Mar 14, 2016 at 20:38 UTC
Try creating a shortcut `clustalw.exe` to `C:\Program Files (x86)\ClustalW2\clustalw2.exe` or add this line to your code `$Bio::Tools::Run::Alignment::Clustalw::PROGRAM_NAME = 'clustalw2';` poj	[reply] [d/l] [select]
Re^10: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 14, 2016 at 22:46 UTC
by adding this line: 'C:\Program' is not recognized as an internal or external command, operable program or batch file. ------------- EXCEPTION ------------- MSG: ClustalW call (C:\Program Files (x86)\ClustalW2\clustalw2.exe align -infile="C:mplamplamplamAppData\Local\Temp\mmbu9X1Xk7\_L046A68Sd" -output=gcg -matrix=BLOSUM -ktuple=3 -outfile="C:mplamplampla\AppData\Local\Temp\mmbu9X1Xk7\QsDsDa0tAB" 2>&1) crashed: 256 STACK Bio::Tools::Run::Alignment::Clustalw::_run C:/Strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm:768 STACK Bio::Tools::Run::Alignment::Clustalw::align C:/Strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm:515 STACK toplevel C:mplamplampla\c3.pl:28	[reply]
Re^11: Can't run Clustalw through Bioperl by Anonymous Monk on Mar 14, 2016 at 23:14 UTC
Now that part is bug in the module, its using string form of system, which is subject to shell interpolation, can be fixed like `## my $commandstring = $self->executable."$instring"."$param_stri +ng"; ## $commandstring .= ' 1>/dev/null' if $quiet; ## $self->debug( "clustal command = $commandstring"); ## ## my $status = system($commandstring); my @command = ( $self->executable, $instring, $param_string +); $self->debug( "clustal command = @command "); my $status = system(@command);` [download]	[reply] [d/l]
Re^12: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 15, 2016 at 00:32 UTC
Re^13: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 15, 2016 at 01:27 UTC
Re^10: Can't run Clustalw through Bioperl by dimitris852 (Acolyte) on Mar 14, 2016 at 21:03 UTC
You mean creating a shortcut of clustalw2.exe and rename it to clustalw.exe? By the way Windows doen't let me create shrotcut in this folder. Suggested me putting the shortcut to Descktop.	[reply]