In the Sali Lab¶
If you are working in the Sali lab, you don’t need to build and install
AllosMod - it is already set up for you as a module. Just run
module load allosmod to load it.
- Python 2.6 or later (Python 3 should also be OK).
- MODELLER. This library expects to be able
to directly import the Modeller Python package (via
import modeller) and to run the Modeller binary (e.g. mod9.15). If you installed Modeller from the
.tar.gzpackage, you will need to set the
LD_LIBRARY_PATHenvironment variables to facilitate this.
- DSSP. It is expected that the
mkdssp binary is in the
- nose is also needed to run the test suite (recommended but not essential).
If you will also be using SAXS profiles (e.g. for the AllosMod-FoXS web service) then you will need:
- ProFit. The
profit binary needs to be in the
In the Sali lab, running
module load modeller dssp profit will get all
of these dependencies.
make test to test the library, and
make install to install it.
In most cases you will need to tell
make where to install (if running on
a Linux cluster, AllosMod will need to be installed on a network-accessible
filesystem) and where any temporary/scratch disks usable by AllosMod are.
(AllosMod needs a ‘local’ scratch disk, accessible by individual jobs on each
node, as well as a ‘global’ scratch disk, on a network-accessible filesystem.)
Do this with something like
make PREFIX=/shared/allosmod GLOBAL_SCRATCH=/scratch install. See
Makefile.include for all make variables that can be configured.