[Bioperl-l] problems getting 1.2 tarball

Jason Stajich jason@cgt.mc.duke.edu
Thu, 9 Jan 2003 11:50:20 -0500 (EST)

On Thu, 9 Jan 2003, Brian Osborne wrote:

> Ewan,
> This proposal to install scripts with PLS suffixes into $SCRIPT_INSTALL/ on
> 'make install' is not mine, though it makes sense to me. I believe it's
> Jason's and Lincoln's idea, though others may have discussed it as well.
Lincoln's idea - he does this in GBrowse - this allows the user upon
install install to set the
#!/usr/bin/perl -w to be whatever the system value is
(/mount/osf1/bin/perl or whatever) and install these ready-to-go scripts
in the PREFIX/bin just like how LWP installs GET,POST scripts .

I think it is a good idea as we push for more utility scripts - I am
putting the general purpose ones that I have written in scripts/utilities,
I am not totally sure we are going to be able to come up with the
appropriate directory naming scheme to localize all of these into (i.e.
graphics, database searching, etc) so I just have thrown in my general
purpose ones into the utility for lack of better ideas.

> You also mentioned the version number insertion idea. Not mine either! Was
> this implemented by Allen Day? bioperl.pod now says it's maintained by
> Allen, that's why I suggest this.
> But I'll given my rendition of it for purposes of discussion. I'd been away
> from Bioperl for a few months and I updated and saw that each *pod document
> now had a partner *PL file. So executing bioperl.PL should create a
> bioperl.pod, where a version number is inserted into the NAME line, drawn
> from a bioperl.conf file. The PL script can also read from the AUTHORS file
> and insert its contents into the *pod file. All reasonable. My only
> suggestion would be to move bioperl.conf, LocalConfig.pm, and the *PL files
> to a separate directory, like conf/ or doc/conf, for a cleaner top-level
> directory. There's no need for the typical user to execute these PL files or

I am fully in agreement with Brian here - these are confusing and don't
need to be in the toplevel.

> change bioperl.conf and the presence of the partnered PL and pod files
> may be confusing, since all the documentation just talks about doing
> things like 'perldoc <some>.pod'. This is analogous to hiding the
> faq.xml file deep in the doc/ directory - don't show it if it's used
> solely to create the file that's actually being read, in this case
> 'FAQ'.
> Question about PL/pod: it looks like biodatabases.PL, biodesign.PL, and
> bioscripts.PL don't create corresponding pod's with version numbers or
> author lists, anotherwords these *PL scripts don't do anything currently.
> Shall we make do them do something useful or remove them?

Allen Day should chime in - maybe they didn't get migrated yet?

> Brian O.
> -----Original Message-----
> From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Ewan Birney
> Sent: Thursday, January 09, 2003 3:23 AM
> To: Brian Osborne
> Cc: bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] problems getting 1.2 tarball
> Brian -
> is the .PLS a standard ending or is this a system you are proposing which
> would work with your version number insertion?
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu