[Bioperl-l] script installation

[Jason Stajich]

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
> ___ _/_/_/_/_/________________________________________________________
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu