Installation on Debian/Ubuntu

Flow is an open source GUI for the analysis of flow cytometry data, written in Python with the wxPython toolkit. It is no longer actively maintained,

[[ Base system ]] sudo apt-get install python-wxgtk2.6 python-numpy python-tables python-scipy python-matplotlib python-networkx python-mdp

[[ Plugins ]]

[ Graphics/ThreeDFrame ] sudo apt-get install python-vtk

[ Statistics/kmeans ] sudo apt-get install python-biopython

[ Statistics/Kde and Statistics/bayes ] sudo apt-get install scons libboost-dev r-mathlib blitz++ lapack3-dev

install the ANN library (for kde)

cd /tmp wget http://www.cs.umd.edu/~mount/ANN/Files/1.1.1/ann_1.1.1.tar.gz tar -xzf ann_1.1.1.tar.gz cd ann_1.1.1/ make linux-g++ cd .. sudo mv ann_1.1.1 /usr/local/src

install the boost numeric binding headers (for bayes)

cd /tmp wget http://news.tiker.net/news.tiker.net/download/software/boost-bindings/boost-bindings-20070826.tar.gz tar -xzf boost-bindings-20070826.tar.gz sudo cp -R boost-bindings/boost/numeric/bindings/ /usr/include/boost/numeric/

alternatively, check out svn repository of boost-sandbox

svn co http://svn.boost.org/svn/boost/sandbox/boost/numeric/bindings ublas_extensions/boost/numeric/bindings sudo cp -R ublas_extensions/boost/numeric/bindings/ /usr/include/boost/numeric/

build the python shared libraries for kde and Bayes where $FLOW is the base directory

sudo apt-get install libboost-python-dev cd $FLOW/src scons install

[ Projections/ica ] sudo apt-get install python-rpy r-base gfortran sudo R

install.packages("fastICA") q()

python-rpy binaries are tied to specific R versions

if the version from the package manager fails (e.g. on Ubuntu 8.02)

uninstall and install from source

sudo apt-get remove python-rpy cd /tmp wget superb-west.dl.sourceforge.net/sourceforge/rpy/rpy-1.02.tar.gz tar -xzf rpy-1.0.2.tar.gz cd rpy-1.0.2 python setup.py build python setup.py install

[Projections/ica2 and pca2 using the Python Modular toolkit]

available for Debian lenny and sid

sudo apt-get install python-mdp

all other distributions

Download tar.gz file from sourceforge http://sourceforge.net/project/showfiles.php?group_id=116959 tar -xzf MDP-2.3.tar.gz sudo python setup.py install

Flow should now be ready to run

cd $FLOW/src python App.py

Fedora Core 9 installation

Packages available using yum

sudo yum install numpy scipy matplotlib hdf5-devel wxPython vtk-python python-setuptools R R-devel rpy

Packages to install from source

1. pytables mkdir src cd src wget http://www.pytables.org/download/stable/pytables-2.0.4.tar.gz tar xzf pytables-2.0.4.tar.gz cd pytables-2.0.4 python setup.py build_ext --inplace sudo python setup.py install exit cd ..

2. networkx wget https://networkx.lanl.gov/download/network/networkx-0.37.tar.gz tar -xzf networkx-0.37.tar.gz cd networkx-0.37 python seutp.py build sudo python setup.py install exit cd ..

3. MDP wget http://voxel.dl.sourceforge.net/sourceforge/mdp-toolkit/MDP-2.3.tar.gz tar xvf MDP-2.3.tar.gz cd MDP-2.3 python setup.py build sudo python setup.py install exit cd ..

4. PyCluster wget http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/Pycluster-1.41.tar.gz tar xzf Pycluster-1.41.tar.tz cd Pycluster-1.41

5. fastICA using R (optional but useful as an example of R integration) sudo yum install gcc-gfortran R

install.packages('fastICA') Follow prompts and quit when done

Download and run Flow

wget http://hg.dulci.org/flow/archive/tip.tar.gz tar xzf tip.tar.gz cd flow-xxxxxxxxxxxxxx (where xxxxxxxxxxxxxx is some machine-assigned label) cd src python App.py

OpenSUSE 10.3 64-bit installation

Add the following repositories to YAST (or other package management tool)

http://download.opensuse.org/repositories/science/openSUSE_10.3/ http://software.opensuse.org/download/repositories/science/openSUSE_10.3/

Install the following using YAST (or other package management tool)

gcc gcc-c++ make python-numpy python-scipy python-setuptools python-tables python-wxgtk python-matplotlib python-matplotlib-wx R-base

Install the following python packages using setuptools

sudo easy_install networkx

Install the following from source

python Cluster library

wget http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/Pycluster-1.41.tar.gz tar -xzf Pycluster-1.41.tar.gz cd Pycluster-1.41/ sudo python setup.py install

R fastICA library

R

ANN library (for kde)

cd /tmp wget http://www.cs.umd.edu/~mount/ANN/Files/1.1.1/ann_1.1.1.tar.gz tar -xzf ann_1.1.1.tar.gz cd ann_1.1.1/ make linux-g++ cd .. sudo mv ann_1.1.1 /usr/local/src

python MDP library

wget http://voxel.dl.sourceforge.net/sourceforge/mdp-toolkit/MDP-2.3.tar.gz tar -xzf MDP-2.3.tar.gz sudo python setup.py install

VTK (python bindings do not appear to work in 64-bit openSUSE 10.3)

wget http://www.vtk.org/files/release/5.2/vtkdata-5.2.0.tar.gz tar -xzf vtkdata-5.2.0.tar.gz wget http://www.vtk.org/files/release/5.2/vtk-5.2.0.tar.gz tar -xzf vtk-5.2.0.tar.gz mkdir VTKBuild cd VTKBuild ccmake ../VTK (set the options as shown) BUILD_EXAMPLES ON BUILD_SHARED_LIBS ON BUILD_TESTING OFF CMAKE_BACKWARDS_COMPATIBILITY 2.4 CMAKE_BUILD_TYPE CMAKE_INSTALL_PREFIX /usr/local VTK_DATA_ROOT < VTKData location - auto-detected > VTK_USE_INFOVIS ON VTK_USE_PARALLEL OFF VTK_USE_RENDERING ON VTK_USE_VIEWS ON VTK_WRAP_JAVA OFF VTK_WRAP_PYTHON ON VTK_WRAP_TCL OFF make sudo make install

Mac OS X 10.5 installation

[[ Base system ]]

Download and install the wxPython binary from http://www.wxpython.org/

Install the binaries for scipy, numpy and matplotlib from http://pythonmac.org/packages/py25-fat/index.html

cd /tmp wget http://pypi.python.org/packages/source/n/networkx/networkx-0.36.tar.gz tar -xzf networkx-0.36.tar.gz cd networkx-0.36 python setup.py build sudo python setup.py install

cd /tmp wget http://www.pytables.org/download/stable/pytables-2.0.3.tar.gz tar -xzf pytables-2.0.3.tar.gz cd pytables-2.0.3 python setup.py build sudo python setup.py install

[[ Plugins ]]

[ Graphics/ThreeDFrame ]

• Installing cmake cd /tmp wget http://www.cmake.org/files/v2.4/cmake-2.4.8.tar.gz tar -xzf cmake-2.4.8.tar.gz cd cmake-2.4.8 ./bootstrap make sudo make install

• Installing VTK cd /tmp cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTK login (respond with password vtk) cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTK checkout VTK mkdir VTKBuild cd VTKBuild ccmake ../VTK options (BUILD_SHARED_LIBS ON; VTK_WRAP_PYTHON ON) Hit 'c' to configure and 'g' to generate Makefiles make sudo make install cd Wrapping/Python python setup.py build sudo python setup.py install export PYTHONPATH=/Library/Python/2.5/site-packages/VTK-5.1.0-py2.5.egg/vtk

[ Statistics/kmeans ] wget http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz

[ Statistics/Kde and Statistics/bayes ]

install the ANN library (for kde)

cd /tmp wget http://www.cs.umd.edu/~mount/ANN/Files/1.1.1/ann_1.1.1.tar.gz tar -xzf ann_1.1.1.tar.gz cd ann_1.1.1/ make macosx-g++ cd .. sudo mv ann_1.1.1 /usr/local/src

install the blitz++ library

cd /tmp wget http://internap.dl.sourceforge.net/sourceforge/blitz/blitz-0.9.tar.gz tar -xzf blitz-0.9.tar.gz cd blitz-0.9 ./configure make sudo make install

install the C++ boost library

cd /tmp wget http://superb-west.dl.sourceforge.net/sourceforge/boost/boost_1_35_0.tar.gz tar -xzf boost_1_35_0.tar.gz cd boost_1_35_0 ./configure make sudo make install

install the boost numeric binding headers (for bayes)

cd /tmp wget http://mathema.tician.de/news.tiker.net/download/software/boost-numeric-bindings/boost-numeric-bindings-20081116.tar.gz tar xzf boost-numeric-bindings-20081116.tar.gz sudo cp -R boost-bindings/boost/numeric/bindings/ /usr/include/boost/numeric/

alternatively, check out svn repository of boost-sandbox

cd /tmp svn co http://svn.boost.org/svn/boost/sandbox/boost/numeric/bindings ublas_extensions/boost/numeric/bindings sudo cp -R ublas_extensions/boost/numeric/bindings/ /usr/include/boost/numeric/

build the python shared libraries for kde and Bayes where $FLOW is the base directory

cd $FLOW/src scons install

[ Projections/ica ]

Install R from source

cd /tmp wget http://cran.r-project.org/src/base/R-2/R-2.6.2.tar.gz tar -xzf R-2.6.2.tar.gz cd R-2.6.2.tar.gz ./configure --enable-BLAS-shlib --with-blas='-framework vecLib' make sudo make install cd src/nmath/standalone make sudo ln -s /Library/Frameworks/R.framework/Resources/R /usr/local/bin/R

Install fastICA

sudo R

install.packages("fastICA")

Install rpy

cd /tmp wget superb-west.dl.sourceforge.net/sourceforge/rpy/rpy-1.02.tar.gz tar -xzf rpy-1.0.2.tar.gz cd rpy-1.0.2 python setup.py build python setup.py install

[Projections/ica2 and pca2 using the Python Modular toolkit] Download tar.gz file from sourceforge http://sourceforge.net/project/showfiles.php?group_id=116959 tar -xzf MDP-2.3.tar.gz sudo python setup.py install

Windows Installation

Note - this was done on a Windows Vista Business Machine with User Access Control (UAC) turned off.

The following binaries have nice Windows installers

Download and install the Enthought binary from http://www.enthought.com/products/epddownload.php Download and install Numeric binary from http://biopython.org/DIST/Numeric-24.2.win32-py2.5.exe Download and install PyCluster binary from http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/Pycluster-1.39.win32-py2.5.exe Download and install Networkx binary from http://pypi.python.org/packages/any/n/networkx/networkx-0.36.win32.exe

Add Python to the Environment path by clicking on the Start icon, then right-clicking on Computer and then "Advanced system settings" on the Tasks pane which will open a System Properties dialog. Click "Environment Variables" and edit "System variables" and add

;C:\Python25;C:\Python25\Scripts

to the end of the Path string.

== Optional install of MDP for ICA and PCA functionality == MDP also has a Windows binary at http://downloads.sourceforge.net/mdp-toolkit, but the link was down when I tried it. If it works for you, install the binary.

If not , download MDP from http://downloads.sourceforge.net/mdp-toolkit/MDP-2.3.zip

Unzip into an appropriate directory, open a Command Prompt, navigate to the MDP-23 folder and type "python setup.py install"

== Note == Executables for Windows 32 and 64 bit DLLs need to be provided, and the Scons script modified to include a section for Windows installations.