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LICENCE

HiFiX is licensed under the General Public License.

DOWNLOAD

You can dowload the latest version HERE.

SYSTEM REQUIREMENTS & DEPENDENCIES

HiFiX was succesfully tested on Linux (Ubuntu up to 14.04, Debian Wheezy 7.0) and Mac OSX (Darwin 10.5.8)

HiFiX does not work with Python 3.x, Python 2.X required
Python modules (already installed by default in Python >=2.7) :

- NumPy
- argparse
- subprocess
- multiprocessing

and
- BioPython

(for local install, set the PYTHONPATH variable to /path_to/module)

Auxiliary software packages (installation required)

- SiLiX (version >= 1.2.10)
- MAFFT
- HMMER3
- Louvain : for this program, there is no proper install procedure. First uncompress this archive and go to the Community_BGLL_CPP directory. Compile with make (NB : on MacOS only, create a dummy file with touch malloc.h, and compile with make CFLAGS+="-I."). Then we suggest three solutions :

  • [RECOMMENDED] copy manually the binaries community, convert and hierarchy in your PATH (in /usr/local/bin for example)
  • add the /path_to/Community_BGLL_CPP directory to your PATH (export PATH=$PATH : /path_to/Community_BGLL_CPP)
  • [EASY] pass the /path_to/Community_BGLL_CPP directory to HiFiX by command line (in this way, the above test procedure will fail... don’t panic)

INSTALLATION

Compilation and installation are compliant with the Python standard procedure

tar zxvf hifix-x.x.x.tar.gz
cd hifix-x.x.x
python setup.py test
python setup.py install

(for local install, add the flag —prefix /path_to/hifix and set PYTHONPATH= /path_to/hifix/lib/python2.x/site-packages)