[Bioperl-l] RE: Installing BioPerl under Mac OS X

Andrew McArdle ajm226 at cam.ac.uk
Wed Oct 20 07:27:12 EDT 2004

Dear Madeleine,

Thank you very much for your valuable advice. You were right, I was trying
to install BioPerl under MacOS, but I was hampered by an insufficient
understanding of Linux, and even less knowledge of Mac OS X. I did follow
some of Steve Cannon's instructions, and they helped for some of the way.
Unfortunately, I am only running Mac OS 10.2.6, so I had to download the
XCode tools. Each obstacle I have navigated so far with regard to the
installation seems to have revealed a new problem. I did try Fink (it was
not preinstalled with Mac OS 10.2 I don't think), but maybe due to lack of
perseverance couldn't even really manage using that.

Ultimately, I decided to be antisocial and work from home, since I have a
dual-boot Windows XP/Mandrake Linux box. The BioPerl installation using CPAN
on Linux was a relative doddle, and then I installed MySQL (again very
simple) and DBI as the Perl adaptor, and everything is working fine. It
would still be nice to have the applications working on Max OS though, since
it is nicer to work in the lab, and when it comes to running scripts that
take several hours or more to complete I would rather have it on the lab

Thanks again for all the information. It may still be necessary at some
point for me to set everything up in the lab.


-----Original Message-----
From: Madeleine Lemieux [mailto:mlemieux at bioinfo.ca]
Sent: 20 October 2004 11:52
To: ajm226 at cam.ac.uk
Cc: bioperl-l at portal.open-bio.org
Subject: Re: Installing BioPerl under Mac OS X


I've just finished installing the latest BioPerl release (1.4) under
Mac OS X 10.3 (10.3.4 when I started but now 10.3.5). Like you, I'm
fairly new at this.

You refer to being a Linux newbie. Are you installing BioPerl under
Linux or OS X? If the former, I can't help since my experience is with
OS X; otherwise, read on.

I found Steve Cannon's instructions useful as a starting point
(http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html). Xcode tools
are pre-installed with OS X 10.3 so I didn't need to do the first step.
You may want to create /usr/local/bin, /usr/local/lib, /usr/local/share
and /usr/local/src directories for your installations since many
programs use this a default locations. Make sure they show up in your
$PATH in ~/.bash_profile (Terminal) or ~/.bashrc (Xterm). That's also
where you need to put some of the environment variables for blast,
amongst others.

Before starting, you might want to do a "fink selfupdate" to get this
very nice package manager up to date. It comes pre-installed with
Panther, I believe, but if not, you can get it from
http://fink.sourceforge.net/. If you use fink to install, it usually
put things under /sw in its own little world which is actually nice if
you're unsure of yourself since it removes the risk of trashing things
in /usr/bin or /usr/lib. Just remember to add /sw/bin to your search

I used fink to install libwww-pm581 and GD. I then forced the
installation of the BioPerl bundle using CPAN. This was necessary as
quite a few of the tests failed but not on things I cared about
especially. I then downloaded the latest BioPerl release and followed
the installation instructions. Worked fine.

I have also installed (following each package's installation
instructions) wwwBlast (latest OS X version from NCBI), t-coffee (the
Unix version, not the Mac one), clustalw (the OS X version) and EMBOSS.
These were all straightforward installations as per instructions. I
never successfully compiled the NCBI C++ Toolbox - my suspicion is that
there are some assumptions made about paths that are incorrect on my
machine and no amount of fiddling with the configure settings helped -
but the C Toolkit (for Unix not Mac) compiled and installed like a
charm, according to instructions in readme.unx.

If you want to go through bptutorial.pl with the graphical debugger
(I've started doing this and I think it's great), you'll need to
install pTk (I downloaded TK800.024 from CPAN.) and then ptkdb (also
from CPAN). I had problems compiling pTk but eventually got it working
(see below). After pTk was up and running, the ptkdb installation went
seamlessly. If you use this, remember: ptkdb has to be run in an xterm
window, not a terminal :-)  (I can't remember whether I had to install
X11 but if so it was from the disks that shipped with my iBook.)

1. Tk looks for perl under /usr/local/bin/perl but it's in
	ln -s /usr/bin/perl /usr/local/bin/perl takes care of that problem.

2. Make reported the following:
	LeMeiLin:~/BioPerl/Tk800.024 $ make
	cd pTk && make DEFINE=""
	cc -c  -I.. -I/usr/X11R6/include -I. -Ibitmaps -I/usr/X11R6/include -g
-pipe 	-pipe -fno-common -DPERL_DARWIN -no-cpp-precomp
-fno-strict-aliasing -I/usr/	local/include -Os   -DVERSION=\"800.024\"
"-I/	System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE"   -Wall
-Wno-	implicit-int -Wno-comment -Wno-unused -D__USE_FIXED_PROTOTYPES__
	In file included from /usr/include/sys/event.h:154,
                  from /usr/include/sys/select.h:71,
                  from tkUnixPort.h:56,
                  from tkPort.h:42,
                  from Xlib_f.c:1:
	/usr/include/mach/mach.h:79: error: parse error before '->' token
	make[1]: *** [Xlib_f.o] Error 1
	make: *** [pTk/libpTk.a] Error 2

	My fix: commented out line 1615 of Lang.h
		(#define panic Tcl_panic)

3. Make then reported:
	--center not a valid option

	My fix: changed POD2MAN_EXE switches --center and --release
	to -c and -r, respectively, in Tk/MMutil.pm line 335

4. I also changed line 5 in demos/widget ("use Tk 800.000") to ("use Tk
800.024") since that's my version.

Sorry! I guess my --verbose switch was on :-)

Good luck,

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