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

[Madeleine Lemieux]

Andrew,

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 
path.

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 
/usr/bin/perl.
	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\" 
-DXS_VERSION=\"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__ 
Xlib_f.c
	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,
Madeleine