These are the generic instructions for installing everything from source, which should work on any kind of Unix, including MacOS-X. There usually are short cuts depending on your flavor/distribution. Ubuntu Linux makes things particularly easy. See the Ubuntu-specific installation instructions. Even though we never cared for it, installation on Windows is actually also possible but requires some tricks -- contact us for help in this case.
Contents Detailed Instruction
- Install required programs
- Install required libraries
- Install PVM - Parallel Virtual Machine
- Install Biskit library
- Next steps
- NOTE 3 NOTE 4 NOTE 5
Install required programs
Note, we assume that your computer has some standard development tools up and running. On Ubuntu, you can install the necessary programs like this:
sudo apt-get install gcc make autoconf libtool gawk
- Python (version 2.5 required, 2.7 recommended)
from rpm or source
install from rpms or debian
- python and (on many systems) python-devel (source / include files) (Ubuntu: python-dev)
from source (works well on pretty much any system)
download from http://www.python.org/
./configure make make install (installs in /usr/local)
Redhat systems are notorious for shipping with old python versions that cannot easily be replaced. In this case, install the latest python from source into, e.g. /usr/local and then push the new python to the top of the search PATH, for example:
ln -s /usr/local/bin/python2.5 ~/bin/python export PATH=~/bin:$PATH
from rpm or debian
install the gnuplot package with your favorite package manager
download from http://www.gnuplot.info/download.html
unpack the tarball and then build, test, and install it:
cd gnuplot-4.2.0 ; ./configure ; make make check make install
Install required libraries
- General note:
Most python libraries are installed with a simple python setup.py install command and will end up in the site-packages folder of your local python installation. If you don't have sudo rights you can also install them into a different location (and set your PYTHONPATH appropriatly, for example:python setup.py install --home ~/local
...will install your python library into ~/local/lib/python.
from rpm or source
With Biskit 2.1 and higher we have switched to the new Numeric incarnation called numpy.
from rpms (Ubuntu package: python-numpy)
download latest numpy version from http://sourceforge.net/projects/numpy/
unpack and install it, e.g.:
tar xvfz numpy-* cd numpy-* sudo python setup.py install
from rpm, deb or source
NetCDF is required by Scientific Python and will usually be installed automatically if you use Debian or RPM package managers.
install from rpms (e.g. SuSE: package netcdf, Ubuntu: libnetcdf3)
./configure --prefix=/usr/local make test make install
Note: On a recent install on an AMD 64bit system Scientific python failed to install if not netCDF was recompiled after setting:
export CPPFLAGS="-fPIC -Df2cFortran" export FFLAGS="-fPIC"
check that x11 and libplot include+library files are installed (a separate x11-devel package in some distros, in Ubuntu you need libplot-dev):
~> ll /usr/lib/libXaw.so lrwxrwxrwx 1 root root 10 2007-05-16 14:36 /usr/lib/libXaw.so -> libXaw8.so
download and install biggles 1.6.6:
wget http://downloads.sourceforge.net/biggles/python2-biggles-1.6.6.tar.gz tar xvf python2-biggles-1.6.6.tar.gz cd cd python2-biggles-1.6.6 python setup.py build sudo python setup.py install
python >>> import biggles >>>
Then paste the following code snippet into your python interpreter:
import biggles, numpy x = numpy.arange(0,10,0.3) p = biggles.FramedPlot() p.add( biggles.Curve(x, numpy.cos(x)) ) p.show()
Consult our biggles troubleshooting guide if you experience any problems!
from rpm, debian or source -- NOTE 3
install from debian or rpms (e.g. Ubuntu: python-biopython)
download from http://www.egenix.com/files/python/mxTextTools.html or from our package mirror
python setup.py install
or install from rpm (e.g. SuSE: python-egenix-mx-base, Ubuntu: python-egenix-mxtools)
download from http://www.biopython.org/ (use latest version!)
python setup.py build python setup.py test python setup.py install
Install PVM - Parallel Virtual Machine
Note: Feel free to skip the following steps if you don't care about parallelization.
- PVM binaries
from source or rpm
- install pvm and pvm-devel from rpm or repositories (preferred!) (Ubuntu: pvm, pvm-dev)
- from source: follow the PVM from source Howto!
- setup PVM environment
shell variables and links
add to .zshenv (example, adapt to your shell):
export PVM_ROOT=/usr/lib/pvm3 ## depends on system export PVM_RSH=/usr/bin/ssh export PVM_ARCH=`$PVM_ROOT/lib/pvmgetarch`
(the variable $PVM_ARCH should match the name of a folder in $PVM_ROOT/lib/ describing the machine architecture -- LINUX or LINUX64 are typical values. In most cases, it is only needed for the compilation of pypvm and can be commented out afterwards. )
In $PVM_ROOT/bin/$PVM_ARCH make links to applications that pvm needs -- biskit requires xterm and python, for example:
cd $PVM_ROOT/bin/$PVM_ARCH ln -s `which xterm` . ln -s `which python` .
- install pypvm
python bindings for PVM
download our repackaged pypvm:
wget http://biskit.pasteur.fr/install/troubleshooting/pypvm_repackaged tar xvfz pypvm_repackaged
python setup.py build python setup.py install
this can turn into a bit of a headache if you run the latter command as sudo which then doesn't know about your $PVM_ROOT and $PVM_ARCH variables. Try the following (replace zsh and .zshrc by your default shell and shell configuration):
sudo zsh source ~/.zshenv python setup.py install
- password-less master -> slave access:
ssh key generation
on the master: If you don't yet have a .ssh/id_dsa.pub file, run:
ssh-keygen -t dsa
Check that there is no .ssh directory on the remote machine (otherwise skip the mkdir .ssh command in the next step).
Copy public key from the master to the slave:
cat ~/.ssh/id_dsa.pub | ssh user@machine "(mkdir .ssh;cat >> .ssh/authorized_keys2)"
on the slave: run:
chmod go-w . .ssh .ssh/authorized_keys2
Check that passwordless login works without providing a password. -- NOTE 4
- Test your PVM installation
See PVM Howto!
Install Biskit library
- get Biskit
fetch a snapshot of the biskit package
Fetch the most current version from GitHub:
git clone https://github.com/graik/biskit.git biskit
Check your firewall settings if you get "connection refused" or "timeout" errors at this step.
Or download last file release from GitHub
Alternatively, you can also download the latest file release from github.
After downloading, unpack it with:
untar xvfz *.tar.gz
- Adapt PYTHONPATH
the Biskit library folder needs to be added to the PYTHONPATH environment variable
Edit your shell configuration file (example for .bashrc or .zshenv):
(Assuming you checked out biskit into your home directory.)
Now you should be able to import the Biskit module in your python scripts.
- The Ubuntu package python-biopython is usually one or two release numbers behind the actual version. If there are any issues with blast searches or other NCBI tools, try installing the current release from source.
- [Resolved] If the biopython test hags at "test_SVDSuperimposer ..." you are suffering from the Numeric/eigenvalue problems. See Numeric Lapack+Atlas.
- Or download and use ssh-keyinstall to set up your system:
Still having problems? Check for firewalls!
Installing Scientific Python on 64bit based Linux systems might be tricky (tested with openSuse 11.1). In order to run this installation, you have to modify the setup.py of Scientific Python on line :
line 48 : "lib/python%s.%s/site-packages/numpy/core/include" to : "lib64/python%s.%s/site-packages/numpy/core/include"
After this modification everything should go fine.