[Bioperl-l] Re: Installing BioPerl under Mac OS X
mlemieux at bioinfo.ca
Wed Oct 20 06:52:28 EDT 2004
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,
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,
/usr/include/mach/mach.h:79: error: parse error before '->' token
make: *** [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 :-)
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