Skip Menu |
 

This queue is for tickets about the bioperl-run CPAN distribution.

Report information
The Basics
Id: 50737
Status: rejected
Priority: 0/
Queue: bioperl-run

People
Owner: Nobody in particular
Requestors: DJIBEL [...] cpan.org
Cc: bug-bioperl-run [...] rt.cpan.org
AdminCc:

Bug Information
Severity: Critical
Broken in:
  • 1.5.2_100
  • 1.6.0
  • 1.6.1
Fixed in: (no value)



CC: bug-bioperl-run [...] rt.cpan.org
Subject: Bug - Bio::Tools::Run::Alignment::Clustalw - patch
Download (untitled) / with headers
text/plain 1.1k
Dear, I have detected some problems on this module (Bio::Tools::Run::Alignment::Clustalw) when I use it from Windows. The executable crashed when there are some spaces on my path files because the system command crash on DOS. To resolv this problem, you have to add double quote in the module around -outfile and -infile values. That is a patch to resolv it. I have tested and it is work well on WinXP, Win2000, Vista with Perl 5.8. --- C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm Fri Oct 9 15:02:04 2009 +++ C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw_new.pm Fri Oct 9 15:05:41 2009 @@ -592,7 +592,7 @@ $instring = "$infile1"; $command = ''; } else { - $instring = " -infile=$infile1"; + $instring = " -infile=". '"' . $infile1 . '"'; } $param_string .= " $infile2"; @@ -775,7 +775,8 @@ next unless (defined $value); my $attr_key = lc $attr; #put params in format expected by clustalw $attr_key = ' -'.$attr_key; - $param_string .= $attr_key.'='.$value; + $param_string .= $attr_key . '=' . '"' . $value . '"'; + #$param_string .= $attr_key.'='.$value; } for $attr ( @CLUSTALW_SWITCHES) { Best Regards, Djibril
Download (untitled) / with headers
text/plain 1.2k
Duplicate of RT 50737. On Thu Oct 22 03:53:51 2009, DJIBEL wrote: Show quoted text
> Dear, > > I have detected some problems on this module > (Bio::Tools::Run::Alignment::Clustalw) when I use it from Windows. The > executable crashed when there are some spaces on my path files because > the system command crash on DOS. > > To resolv this problem, you have to add double quote in the module > around -outfile and -infile values. > > That is a patch to resolv it. I have tested and it is work well on > WinXP, Win2000, Vista with Perl 5.8. > > > > --- C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm Fri Oct 9 > 15:02:04 2009 > +++ C:/Perl/site/lib/Bio/Tools/Run/Alignment/Clustalw_new.pm Fri Oct > 9 15:05:41 2009 > @@ -592,7 +592,7 @@ > $instring = "$infile1"; > $command = ''; > } else { > - $instring = " -infile=$infile1"; > + $instring = " -infile=". '"' . $infile1 . '"'; > } > $param_string .= " $infile2"; > > @@ -775,7 +775,8 @@ > next unless (defined $value); > my $attr_key = lc $attr; #put params in format expected by clustalw > $attr_key = ' -'.$attr_key; > - $param_string .= $attr_key.'='.$value; > + $param_string .= $attr_key . '=' . '"' . $value . '"'; > + #$param_string .= $attr_key.'='.$value; > } > > for $attr ( @CLUSTALW_SWITCHES) { > > Best Regards, > > Djibril


This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

Please report any issues with rt.cpan.org to rt-cpan-admin@bestpractical.com.