[Bioperl-l] script installation

[Lincoln Stein]

Just a bit of history here.  The idea of storing perl scripts as templates 
appeared in Perl 5.0, and the system was designed around make transforming 
.PL into .pl files.  Unfortunately on Windows and other case-insensitive file 
systems, .PL and .pl are the same.  So I changed the suffix to .PLS.

Lincoln

On Tuesday 11 March 2003 09:47 am, Jason Stajich wrote:
> The whole point is this:
> Some people don't have perl installed in /usr/bin/perl.
>
> The .PLS files are intended to be sort of like templates where you can
> plug in the correct perl path in addition to installing them in a specific
> system script directory (/usr/local/bin, /lab/bin, or /home/me/scripts if
> you like)
>
> This conversion is coded in the Gbrowse Makefile.PL because this is how
> Lincoln makes the gbrowse.PLS into gbrowse and the process_wormbase.PLS
> to process_wormbase.pl.
> Basically there is a bit here in the GBrowse Makefile.PL which is passed
> into the WriteMakefile routine:
>              PL_FILES       => {
>
> 'bin/process_sgd.PLS' => 'bin/process_sgd.pl',
> 'bin/process_gadfly.PLS' => 'bin/process_gadfly.pl',
> 'bin/process_wormbase.PLS' => 'bin/process_wormbase.pl',
> 'bin/process_ncbi_human.PLS' => 'bin/process_ncbi_human.pl',
> 'gbrowse.PLS'  => 'gbrowse',
> 'gbrowse_img.PLS'  => 'gbrowse_img',
> }
>
> This all stemmed from Lincoln explaining it can be annoying for people
> with non-standard perl locations if all the scripts expect to be run from
> /usr/bin/perl
>
> There is a processPL routine that is defined in ExtUtils::MakeMaker and
> implemented by the various OS dependent implementations of MakeMaker which
> already does this transformation I believe - you can override it as
> Lincoln does in Gbrowse to accomplish some other transformations (perhaps
> insert a VERSION number as well if we wanted).  This all may be as simple
> as adding the hash above to the WriteMakefile arguments.  I just haven't
> had the opportunity to really try and debug it.  If no one else wants to
> give the magic a try I can see about it at the end of the week.
>
> -jason
>
> On Tue, 11 Mar 2003, Brian Osborne wrote:
> > Heikki,
> >
> > > Shouldn't that README, or something similar, be in scripts directory
> > > rather than further down?
> >
> > Yes.
> >
> > >Should we try the new scripts already in 1.2.1 release? I thought that
> > > was the intension.
> >
> > Yes, we should.
> >
> > >Also, I've written the documentation for several scripts assuming that
> > >the name conversion will be xxx.PLS -> xxx (and not xxx.pl). What is
> > >correct?
> >
> > I don't know.
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: Heikki Lehvaslaiho [mailto:heikki at ebi.ac.uk]
> > Sent: Tuesday, March 11, 2003 9:03 AM
> > To: Brian Osborne
> > Cc: Bioperl
> > Subject: Re: [Bioperl-l] script installation
> >
> > Shouldn't that README, or something similar, be in scripts directory
> > rather than further down?
> >
> > Also, I've written the documentation for several scripts assuming that
> > the name conversion will be xxx.PLS -> xxx (and not xxx.pl). What is
> > correct?
> >
> > Should we try the new scripts already in 1.2.1 release? I thought that
> > was the intension.
> >
> >         -Heikki
> >
> > On Tue, 2003-03-11 at 13:23, Brian Osborne wrote:
> > > Lincoln and Jason,
> > >
> > > The README in scripts/utilities says:
> > >
> > > This directory is for robust scripts which have documentation,
> > > cmdline arguments, and can be used in a production environment.
> > > Their extensions will be renamed .pl and will be installed in
> > > the SCRIPT_INSTALL directory as defined in the Makefile.PL
> > > configuration.
> > >
> > > We should probably go ahead and implement this, or temporarily remove
> > > this README.
> > >
> > > If you'd like to proceed with the former I can make sure that the
> > > script installation is documented in the appropriate places, and I'll
> > > also go
> >
> > ahead
> >
> > > and test all the scripts in scripts/ as best as I can, as promised.
> > > Your thoughts?
> > >
> > > Brian O.
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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