[Bioperl-l] New Fink Bioperl dependency installer, etc.

[Steven Cannon]

I've been maintaining a site describing my Bioperl install experiences 
on Mac OS X 
( http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html ), and would 
like to keep it up to date by getting feedback from other OS X users. In 
particular, there are two install options that I would like to hear more 
about: the CPAN.pm BioPerl::Bundle, and a new Fink Bioperl dependency 
installer by Christopher Dithi (Thanks! - this should be an ideal 
solution for OS X).

There is an OS X - specific problem with CPAN (see below). The Fink 
"bioperl-pm" is currently in the "unstable" branch, meaning that it 
needs more testing. I would also like to know whether the new version of 
the OS (10.2) causes any problems, either in existing or new 
installations. Here's what I say on my page -- and I'll update this as I 
hear other peoples' experiences with CPAN or Fink.
===
  There are at least three quite distinct options for installing the 
BioPerl dependencies on OS X. You can 1) do it "from scratch," following 
the instructions on this page, or 2) you can use the CPAN.pm module and 
BioPerl::Bundle, which should install almost all of the dependencies 
nearly automatically, or 3) you can try the new Fink bioperl-pm package, 
which also should install almost all of the dependencies nearly 
automatically. Unfortunately, none of these options is entirely without 
a certain amount of hassle and risk. In order, here are the options in 
more detail:

1) Doing the installations manually gives you the most control, but 
there are a few pitfalls here and there (particularly, see the note 
about "HEAD" below, under "LWP.")

2) CPAN.pm is a wonderful creation, but I have been frustrated by it on 
OS X. In particular, the last time I tried to install CPAN.pm itself (in 
July, 2002), it tried to update my version of Perl to 5.80 -- which 
would seem like a virtuous thing, but the Perl reinstallation process 
itself was long and arduous, and didn't work for me (it caused me no 
problems with the default installation, but 5.80 didn't "take.") And 
then when I tried to use it to install BioPerl::Bundle, it tried AGAIN 
(and without asking or giving me the option to refuse) to install 5.80. 
That said, the dependencies did install correctly. However, unless 
someone knows how to circumvent this problem, I can't recommend 
BioPerl::Bundle on OS X. (And if someone knows a way around this 
problem, please let me know! Actually, to investigate, try 
http://www.scriptdigital.com/divers/frontiermonitor.html -- which looks 
like a solution).

3) The Fink option should be the best solution, because the Fink package 
manager is explicitly designed for OS X. It also installs everything in 
its own private directory (/sw), so there is essentially no danger of 
overwriting important Unix utilities and libraries. The bioperl-pm 
package is new, and I haven't tested it, so I (and the package 
maintainer, Christopher Dithi) would be interested to hear how it goes. 
As of August, 2002, the Fink bioperl-pm is in the "unstable" branch, 
meaning that it has not been well tested. You can help!
===
- Steven Cannon