Christian Meesters wrote:
I just installed Ubuntu 7.04 on one machine and tried to get modeller running. I tried an installation from source as well as using the rpm. Actually modeller itself is installed, but the python module is not available. The only python-installation I have is 2.5 and I would rather not work with 2.3. Last time I installed modeller I had the module running with python 2.4, so I guess running with 2.5 should be possible, too. (There are no .so-files I could get into the python path manually.) Did anyone try to install modeller on Ubuntu/Debian or alike and has a hint for me?
Ubuntu and Debian use .deb packages rather than RPMs, so to install the RPM on such a system you should either first convert it to a .deb using the 'alien' tool, or if you're sure your system has the necessary prerequisites for Modeller, you can install the RPM with the --nodeps option. This latter solution should also work on other non-RPM systems such as Gentoo.
You could alternatively install from the .tar.gz (which is also a binary package, not source) but in this case you'd have to make symlinks yourself or otherwise set LD_LIBRARY_PATH and PYTHONPATH so that the Python module works. The RPM makes symlinks to put the Python module in /usr/lib/python2.3/site-packages/ and writes the dynamic library search path (rpath) into the .so so that you do not need to set LD_LIBRARY_PATH.
As regards Python 2.5, the _modeller.so module provided with Modeller 9v1 works for Python 2.3 and 2.4, but not for 2.5. This is because the Python ABI did not change between 2.3 and 2.4, but it did for 2.5 for some of their 64-bit support. So you will you have to rebuild the Python interface if you want to use Python 2.5. This is pretty easy to do - simply go to the src/swig/ directory of your Modeller installation (found under /usr/lib/modeller9v1/ with RPM installs) and see the README there. You will need to have SWIG 1.3.31 installed in addition to the Python headers and a C compiler. You should be able to build a new _modeller.so compatible with Python 2.5, which you should copy into /usr/lib/python2.5/site-packages/ (or /usr/lib64/... on 64-bit systems). You will additionally need to symlink the modlib/modeller directory to the Python 2.5 site-packages dir, just as is currently done for the 2.3 and 2.4 installs. For it to work correctly, you will need to either set LD_LIBRARY_PATH or pass -Wl,-rpath,/usr/lib/modeller9v1/lib/i386-intel8 or similar when you link the .so.
Let me know if you run into any more problems. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage