Installation notes¶

RedHat 64bit¶

(as of September 2010)

Install cython:

$ pip install cython

Download and install a binary distribution of HDF5.

$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.5-patch1.tar.gz
$ ./configure --prefix=<dir>
$ make
$ make install

Also:

$ export HDF5_DIR=<dir>

so that pytables can find it.

Also install LZO and remember to do:

$ export LZO_DIR=<dir>

Download cgkit-1.2.0 from sourceforge.

Use pyrex to recompile cgtypes:

$ cd cgkit-1.2.0
$ pyrex cgtypes.pyx
$ python setup.py install

At this point:

$ cd flydra
$ python setup.py develop

motmot.FastImage cannot be installed, so you have to do a “light” installation.

Apart from that, everything else can be installed.

(as of October 2010)

Before installing pytables, you have to install the lzo library, otherwise you won’t be able to read some compressed files created by flydra.

Here’s a suitable sequence of commands:

$ sudo apt-get install liblzo2-dev
$ sudo apt-get install libbzip2-dev
$ pip install numexpr=1.3
$ pip install tables