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

[Steven Cannon]

On Wednesday, September 4, 2002, at 12:02 PM, Hilmar Lapp wrote:

> I used CPAN, but not BioPerl::Bundle (I just installed the various 
> dependencies; I work on the cvs HEAD). It does try to update Perl at 
> some point, but you can interrupt that step (that's what I did: ^C) and 
> it just carries on with the other modules. As far as I can tell, it 
> works.
OK. I might add a note to this effect.

> The problem with LWP is still there, it did override my system head (do 
> you happen to know where I can get the original one? Can you send me 
> yours?)

You can recover the system 'head' in by copying it from the OS X install 
CD. This might not be obvious, because the true contents of the install 
CD is hidden somehow by the ordinary browser view, but you can see 
what's really there from the command line - for example,

% cd '/Volumes/Mac OS X Upgrade CD'
% ls
       Applications         System               etc                  sbin
       Desktop DB           Welcome to Mac OS X  mach                 tmp
       Desktop DF           bin                  mach_kernel          usr
       Library              dev                  private              var
% ls usr/bin/head
       usr/bin/head

I am not clear, however, what happens when LWP then tries to use its own 
HEAD, but finds head. In any case, my Bioperl and system seem to be OK 
with just 'head' in /usr/bin.

> I tried to install some perl packages and their dependencies with Fink, 
> but wasn't very happy with the results. E.g., some packages (GD for 
> example, MySQL) required C-libs to be available; first, Fink didn't 
> have the required versions, and second after installing it myself it 
> didn't appreciate the stuff being there now. That was all 2 months ago, 
> so things may be different by now.

The Fink bioperl-pm is newer than this, so the process should be 
different now. I don't think that this package installer takes care of 
GD, though. I added instructions to the bottom of my site indicating how 
I dealt with GD, gd, and libpng and libjpeg. This is one that I wasn't 
able to do manually -- I ended up using Fink, as it turns out, but from 
the stable Fink branch, using 'fink install gd'.

- Steven Cannon

> 	-hilmar
>
> On Wednesday, September 4, 2002, at 08:29  AM, Steven Cannon wrote:
>
>> 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
>>
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>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>