[Bioperl-l] Bioperl-run Wrappers

[Jason Stajich]

There is such a method in the Wrapper interface - it is implemented for 
tools (exe) that support outputting the version in some way. e.g. here 
is implementation for infernal (Bio::Tools::Run::Infernal)

=head2  version

  Title   : version
  Usage   : $v = $prog->version();
  Function: Determine the version number of the program (uses cmsearch)
  Example :
  Returns : float or undef
  Args    : none

=cut

sub version {
     my ($self) = @_;
     return unless $self->executable;
     my $exe = $self->executable;
     my $string = `$exe -h 2>&1`;
     my $v;
     if ($string =~ m{Infernal\s([\d.]+)}) {
         $v = $1;
         $self->deprecated(-message => "Only Infernal 1.0 and above is 
supported.",
                           -version => 1.006001) if $v < 1;
     }
     return $self->{'_progversion'} = $v || undef;
}



Ben Bimber wrote:
> Hi Chris,
>
> I actually was referring to the software version of the executable
> itself, not the perl code.  for example, I added something like this
> to a mosaik wrapper I made:
>
> sub version {
> 	my $self = shift;	
> 	my ($out, $err);
> 	IPC::Run::run([$self->executable, '-h'], '>', \$out, '2>', \$err);
> 	my @out = split("\n", $out);
> 	my $version = join(';', grep( /^Mosaik/i, @out));
> 	$version =~ m/^.*0m ([\d\.]*)\b/i;
> 	return "Mosaik Version: $1\n";
> 	
> }
>
> It runs the executable, parses the output (which is specific to mosaik
> in this case) and returns it.  I had an issue with a tool version
> recently, so I decided it was probably a good idea to start recording
> them with pipelines.  In hindsight version() is probably the wrong
> name since it's confusing with perl's VERSION, but maybe exe_version()
> or something makes sense.  I would personally find it useful if there
> were a standard, but optional method across BioPerl wrappers to do
> this sort of thing.  implementing it would be optional per wrapper.
> all it would really need to do it return a string.
>
> -Ben
>
>
>
>
>
>
>
>
>
> On Fri, Feb 4, 2011 at 3:19 PM, Chris Fields<cjfields at illinois.edu>  wrote:
>> On Jan 28, 2011, at 12:18 PM, Ben Bimber wrote:
>>
>>> Hello,
>>>
>>> I'm using CommandExts to wrap a number of tools.  In a pipeline I was
>>> looking to make the tools log their current version.  I realized that
>>> instead of using run() in a unique way for each tool, perhaps there
>>> should be a consistent method that gets called and returns a version
>>> string.  because obtaining this version string is specific to the
>>> tool, perhaps each wrapper could provide a version() method that runs
>>> the appropriate command on the executable, parses, then returns some
>>> string.  has something like this been discussed?  have others already
>>> solved this?
>>>
>>> Thanks,
>>> Ben
>> (apologies for the late response, maybe you worked it out?)
>>
>> If you mean a version string for the wrapped tool, there is a Bio::Tools::Run::WrapperBase method called version() I believe (not implemented for obvious reasons, but implemented by each wrapper as needed).  If you want a specific version of the module (say, an API version) you may want to assign $VERSION or create a new global ($API_VERSION, perhaps) in case it conflicts with the BioPerl core version.
>>
>> chris
>>
>>
>>
>
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-- 
Jason Stajich