Sunday, June 22, 2008

Install libsbml on Ubuntu

I have changed OS to Ubuntu 8.04(hardy), so everything I installed and configured on my old FedoraCore4 were lost

>_< :-(

Now I'm installing libsbml.

./configure complained that C++ compiler cannot produce executables. So I installed "build-essential".

Then ./configure complained following:
*** Could not find 'xml2-config' in directory yes/bin/.
*** Please check that the PATH supplied to --with-libxml=PATH
*** is of the form '/usr/local' and not '/usr/local/lib'; in
*** other words, omit the 'lib' part of the name. The 'configure'
*** utility will append 'lib' to the given path automatically.

I googled, and installed "libxml2-dev".

Then I configured successfully.
./configure --with-python

But make produces a lot of errors. This is because Python developer tools has not been installed.
apt-get install python-dev

Compilation succeeded this time!

make
make install

ldconfig

After this, run python, run "from libsbml import *", command succeed!

Saturday, June 7, 2008

Install Python API to libsbml

I installed Python API to libsbml, the famous SBML library.

First build libsbml with "--with-python" during configure, the libsbml library is installed on /usr/local/lib/ by default, and the Python API is installed on /usr/local/lib/python2.4/site-packages/libsbml;

Then add following line to .bashrc:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
export PYTHONPATH=/usr/local/lib/python2.4/site-packages/libsbml:/usr/local/lib/python2.4/site-packages

This way python can import libsbml!