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INSTALL-TAPIR
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INSTALL-TAPIR
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#
###########################################################################
###########################################################################
# General
INSTALL:
Dependencies:
- 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
Install Python (e.g. version 2.7) from http://www.python.org/getit/
# 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/
Get numpy (numpy-MKL-1.7.2rc1.win32-py2.7.exe)
Get PyQt (PyQt-Py2.7-x32-gpl-4.9.6-1.exe)
Get PyQwt (PyQwt-5.2.1-py2.7-x32-pyqt4.9.6-numpy1.7.1.exe)
Get guiqwt (guiqwt-2.3.1.win32-py2.7.exe)
Get guidata (guidata-1.6.1.win32-py2.7.exe)
# Open command prompt, go to your home
# This assumes you have a git and svn client. If you dont, one essay solution
# on windows for this is to use http://downloadsvn.codeplex.com/ to checkout
# the pymzml and msproteomicstools projects.
cd \my\home\dir
# download and install pymzml using the following link:
# https://github.com/hroest/pymzML/archive/Release_0.7.5.zip
# open a cmd.exe window and navigate to the download location
C:\Python27\python.exe setup.py install
#download msproteomicstools
svn checkout http://msproteomicstools.googlecode.com/svn/trunk/ msproteomicstools
cd msproteomicstool
# Edit ./gui/openswath/AlignmentGUI.py and set USE_GUIQWT to False (replace "True" with "False")
C:\Python27\python.exe gui\openswath\AlignmentGUI.py
###########################################################################
###########################################################################
# Mac
# 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
2. Install Homebrew
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
brew doctor
3. Dependencies
brew install python
brew install gfortran
brew install numpy
brew install scipy
4. Add to ~/.bash_profile
export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
5. 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
6. Install pymzML
cd /tmp
git clone https://github.com/hroest/pymzML
cd pymzML
sudo python setup.py install
cd ..
sudo rm -rf pymzML