[Bioperl-l] problems getting 1.2 tarball

Brian Osborne brian_osborne@cognia.com
Thu, 9 Jan 2003 09:32:45 -0500


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.

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
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?

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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