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-0.9.2.tar.gz
Install the python module and scripts:
cd BornProfiler
python setup.py install
(see 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.