Building and installing BornProfiler¶
BornProfiler consists of a Python package bornprofiler and a
a stand-alone executable draw_membrane2. The Python package is
needed to set up the calculations and draw_membrane2 is needed as
a helper tool for apbs; hence it needs to be installed on the same
machine where apbs is going to run.
Installation from Source¶
Unpack the tar ball:
tar zxvf BornProfiler-1.0.tar.gz
Install the python module and scripts:
cd BornProfiler
python setup.py install --user
(--user might only work for Python 2.6; look at the output of
python setup.py install --help for guidance on what your options
are.)
Compile the customized (and improved) version of draw_membrane
named draw_membrane2:
mkdir BUILD && cd BUILD
cmake -D CMAKE_INSTALL_PREFIX=$HOME -D CMAKE_BUILD_TYPE=Release ../src/drawmembrane
make
make install
The make install step will install the executable
draw_membrane2a under CMAKE_INSTALL_PREFIX/bin; change
CMAKE_INSTALL_PREFIX if you prefer another location.
(cmake is not really needed; if you don’t have it try the following:
gcc ./src/drawmembrane/draw_membrane2a.c -o draw_membrane2a -lm -lz
and install manually in a place where you or your shell can find it.)
Note
draw_membrane2a also needs to be installed on the machine
where you want to run your BornProfiler jobs: it will run
together with apbs. If you are going to run you
calculations on a cluster then draw_membrane2a (and
apbs) need to be both installed on the cluster.
Configuration¶
Finalize your installation by running
apbs-bornprofile-init.py
This should tell you that it set up a configuration file
~/.bornprofiler.cfg and a number of directories.
The default ~/.bornprofiler.cfg looks like this:
[DEFAULT]
configdir = ~/.bornprofiler
templatesdir = %(configdir)s/templates
qscriptdir = %(configdir)s/qscripts
[executables]
apbs = apbs
drawmembrane = draw_membrane2a
The file can be edited in a text editor. For instance, one can add the
full path to the apbs and draw_membrane2a executable binaries.
Any other variables used in run configuration input files can also be added here and will be used as defaults.
Advanced use: You can drop templates for run scripts into qscriptdir and have the BornProfiler package pick them up automagically.