Table of Contents

• Requirements
  • Binary Installation
    • Detailed Directions (Binary)
  • Using Python Source
    • Detailed Directions (Python Source)
      • Windows
      • Mac OS X/Linux
• Motivation
• Tutorial
• Change Log
• Contributors
• License

Should work with no dependencies.

1. Download the binary and extract it, keeping the directory structure intact.
2. Make sure all files are executable
   • On Windows, this should be default
   • On Linux/Mac OS X, this should be:

   chmod +x <file>
   

3. Execute the program

• Python 2.7 or 3.4
• pip
• [Wheel] (https://pypi.python.org/pypi/wheel)
• [PySide] (https://pypi.python.org/pypi/PySide)
• [NumPy] (https://pypi.python.org/pypi/numpy)
• [SciPy] (http://www.scipy.org/)
• [six] (https://pythonhosted.org/six/)
• [Cython] (http://cython.org/)
• [Numexpr] (https://github.com/pydata/numexpr)
• [PyTables] (http://www.pytables.org/)
• [Requests] (http://docs.python-requests.org/en/master/)
• [XlsxWriter] (https://pypi.python.org/pypi/XlsxWriter)

OR

• [OpenPyXl] (https://pypi.python.org/pypi/openpyxl)

1. Make sure Python is added to the path, or type the full path to the Python executable.

2. Install pip by downloading get-pip.py

3. Just run the binary and then install Wheel.

4. For PySide, Six, Requests, and XlsxWriter (or OpenPyXl), install with, replacing "" with the package name.

   python -m pip install <package>
   

5. NumPy, SciPy, Numexpr, and PyTables:

   • Windows Only: Download wheel files from http://www.lfd.uci.edu/~gohlke/pythonlibs/
     • Do NOT rename the wheel files
     • Run the above installer command, replacing "" with full path to the wheel file
   • Mac OS X/Linux: Install these packages via pip

6. Launch xldiscoverer.pyw with any Python launcher.

   • Ex:.

   python xldiscoverer.pyw
   

python get-pip.py
python -m pip install wheel
python -m pip install PySide, XlsxWriter, requests, six
python -m pip install numpy-package.whl
python -m pip install cython-package.whl
python -m pip install numexpr-package.whl
python -m pip install scipy-package.whl
python -m pip install pytables-package.whl

python get-pip.py
sudo pip install wheel
sudo pip install PySide, XlsxWriter, requests
sudo pip install cython numpy scipy numexpr pytables

Tutorial To XL Discoverer

Although the advancement of cross-linking mass spectrometry and its application to the analysis of protein complexes in vivo have been tremendous, the lack of automated tools for MS identification and quantification have stalled its growth. Xl Discoverer aims to provide an automated framework in a standalone application for crosslinking mass spectrometry identification and analysis.

• Alex Huszagh

Copyright (C) 2015 Alex Huszagh https://github.com/Alexhuszagh/xltools/

XL Discoverer is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This xlDiscoverer is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with xlDiscoverer. If not, see http://www.gnu.org/licenses/.