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

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The Basics
Id: 50363
Status: resolved
Priority: 0/
Queue: bioperl-run

People
Owner: Nobody in particular
Requestors: DJIBEL [...] cpan.org
Cc:
AdminCc:

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



Subject: Bug - Bio::Tools::Run::Alignment::Clustalw - patch
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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
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This is based an old version of the module (much of the code has been cleaned up since then). Please resubmit a patch against the latest run version (1.6.0). On Fri Oct 09 09:24:06 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
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On Wed Oct 21 23:49:11 2009, cjfields wrote: Show quoted text
> This is based an old version of the module (much of the code has been > cleaned up since > then). Please resubmit a patch against the latest run version > (1.6.0).
I have submitted a partial fix for this to bioperl svn using the information from your patch, but attached the patch is still significantly out of date. Feel free to reopen this bug or file another one if the problem persists.


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