[Bioperl-l] Installing OS X dependencies

[Todd Richmond]

On 6/30/01 12:34 PM, "Steven Cannon" <cann0010@tc.umn.edu> wrote:

> Bioperl 0.7.1 installed nicely on my Mac OS X, but I have found that
> installing the dependencies is a challenge (particularly for me as a
> *nix novice). I have found OS X binaries or installs for Clustalw, ncbi,
> Xfree86, and Lesstif (open source Motif clone, which has libraries the
> ncbi Toolkit may use?) But I have not been able to install t-coffee. I
> suspect that only small changes need to be made to the makefiles, but I
> don't know what those changes should be to get the install working on
> Darwin. Advice?
> 

Here's what my "install" file looks like:

-------------------------------------
cd t_coffee_source
make clean
make -i CC="cc -Dvfree=my_vfree" USER_BIN=../bin/ all
cd ..
cd ./lalign
make clean
make -i CC=cc USER_BIN=../bin/ all
cd ..
./bin/test.pl

-------------------------------------

The important change here is the "-Dvfree=my_vfree" portion. If you don't
redefine the vfree variable for the compiler, make complains about symbols
that are defined multiple times (if I remember correctly - I installed it
awhile ago). Let me know if this doesn't work, and I'll try to figure out if
I had to do something else as well.


-- 
Todd Richmond                    http://cellwall.stanford.edu/todd
Carnegie Institution             email: todd@andrew2.stanford.edu
Department of Plant Biology      fax: 1-650-325-6857
260 Panama Street                phone: 1-650-325-1521 x431
Stanford, CA 94305