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INSTALL-TAPIR.md

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General Information

This document contains information on how to install TAPIR from source. Binaries are available for Windows and Mac OSX at the project homepage which is what you should try first before proceeding here.

Dependencies for TAPIR are the following:

  • pymzML (from https://github.com/hroest/pymzML/archive/Release_0.7.5.zip)
  • Python >= 2.5
  • numpy / scipy
  • PyQt4 >= 4.3
  • PyQwt >= 5.2
  • PIL (Python Imaging Library, maybe not necessary...)
  • guidata
  • guiqwt

Linux install

  • Debian/Ubuntu/ArchLinux: guiqwt should be packaged, basically install these packages
sudo apt-get install python python-numpy \
     python-qt4 python-qwt5-qt4 python-guiqwt
  • RedHat: PyQwt, PyQt, scipy, numpy, python-imaging should be the packages

Then install the pymzml and msproteomicstools:

git clone https://github.com/pymzml/pymzML.git
python setup.py install
svn checkout http://msproteomicstools.googlecode.com/svn/trunk/ msproteomicstools
cd msproteomicstool

Windows

First install Python (e.g. version 2.7) from http://www.python.org/getit/ or through Anaconda https://www.continuum.io/downloads

then go to the following website and download these binary packages (the following assumes 32 bit window, for 64 bit please choose the appropriate package):

http://www.lfd.uci.edu/~gohlke/pythonlibs/

  1. Get numpy (numpy-MKL-1.7.2rc1.win32-py2.7.exe)
  2. Get PyQt (PyQt-Py2.7-x32-gpl-4.9.6-1.exe)
  3. Get PyQwt (PyQwt-5.2.1-py2.7-x32-pyqt4.9.6-numpy1.7.1.exe)
  4. Get guiqwt (guiqwt-2.3.1.win32-py2.7.exe)
  5. Get guidata (guidata-1.6.1.win32-py2.7.exe)

Next, open a command prompt (type cmd.exe in your search bar in Windows and click on it) and go to your home directory:

cd \my\home\dir

If you do not have an SVN or git client, one essay solution on Windows is to use http://downloadsvn.codeplex.com/ to checkout the pymzml and msproteomicstools projects.

Next, download and install pymzml using the following link:

https://github.com/hroest/pymzML/archive/Release_0.7.5.zip

Then navigate to the download location:

C:\Python27\python.exe setup.py install

next, download msproteomicstools

svn checkout http://msproteomicstools.googlecode.com/svn/trunk/ msproteomicstools
cd msproteomicstool

then edit gui\openswath\AlignmentGUI.py and set USE_GUIQWT to False (replace "True" with "False"). This should fix the script and you can start TAPIR

C:\Python27\python.exe gui\openswath\AlignmentGUI.py

Mac OS X

Thanks to George Rosenberger

This install was tested on OS X 10.8

  1. Install msproteomicstools
svn checkout http://msproteomicstools.googlecode.com/svn/trunk/ msproteomicstools-read-only
  1. Install Homebrew
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew doctor
  1. Dependencies
brew install python
brew install gfortran
brew install numpy
brew install scipy
  1. Add the following to ~/.bash_profile
export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
  1. Install Python and Qt dependencies
source ~/.bash_profile
pip install numpy
pip install scipy

brew install pyqt
brew install pyqwt

pip install guiqwt
pip install guidata
  1. Install pymzML
cd /tmp
git clone https://github.com/hroest/pymzML 
cd pymzML
sudo python setup.py install
cd ..
sudo rm -rf pymzML