Difference between revisions of "LipidXplorer Installation"
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| − | LipidXplorer | + | '''Note:''' The current package of LipidXplorer is compatible with '''Microsoft Windows''' only. A Linux version has to be compiled first. This should be not a big problem. If anyone is interested, please write me. |
| − | |||
| − | ==== | + | |
| − | LipidXplorer | + | ====Installation for Windows==== |
| − | * Python 2.6 [http://www.python.org/ftp/python/2.6. | + | LipidXplorer '''32Bit''' |
| + | * Python 2.6 [http://www.python.org/ftp/python/2.6.6/python-2.6.6.msi here] !Note! Python version has to be >= 2.6.6 | ||
* wxPython 2.8 (for Python 2.6) [http://downloads.sourceforge.net/project/wxpython/wxPython/2.8.11.0/wxPython2.8-win32-unicode-2.8.11.0-py26.exe?use_mirror=mesh&ts=1280922921&r=http://www.wxpython.org/download.php here] | * wxPython 2.8 (for Python 2.6) [http://downloads.sourceforge.net/project/wxpython/wxPython/2.8.11.0/wxPython2.8-win32-unicode-2.8.11.0-py26.exe?use_mirror=mesh&ts=1280922921&r=http://www.wxpython.org/download.php here] | ||
* numPy (for Python 2.6) [http://sourceforge.net/projects/numpy/files/NumPy/1.5.1/numpy-1.5.1-win32-superpack-python2.6.exe/download here] | * numPy (for Python 2.6) [http://sourceforge.net/projects/numpy/files/NumPy/1.5.1/numpy-1.5.1-win32-superpack-python2.6.exe/download here] | ||
| − | + | LipidXplorer '''64Bit''' | |
| − | + | * Python 2.7 [http://www.python.org/ftp/python/2.7.12/python-2.7.12.amd64.msi here] | |
| + | * wxPython 2.8 (for Python 2.7) [http://downloads.sourceforge.net/wxpython/wxPython2.8-win64-unicode-2.8.12.1-py27.exe here] | ||
| + | * install Python 2.7 and wxPython 2.8 | ||
| + | * download the lipidxplorer third party dependencies [https://wiki.mpi-cbg.de/lipidxscr/images/d/d1/Lipidxplorer_additional_installation.zip here] | ||
| + | ** unzip it to a location of your choice | ||
| + | ** double click on <code>install_dependencies.py</code> | ||
| + | ** after the installation finished you can delete the unzipped folder - it is not needed any longer | ||
| + | ** if this fails, you can manually install the dependencies: | ||
| + | *** download <code>pip</code>: [https://bootstrap.pypa.io/get-pip.py get-pip.py] | ||
| + | *** install <code>pip</code> from cmd line with <code>Python get-pip.py </code> | ||
| + | *** download numPy (for Python 2.7 64Bit): Since Numpy is officially not supported for 64Bit there is an unofficial version [http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy here] which can be used and installed. Please select ''numpy-<version>+mkl-cp27-none-win_amd64.whl'' where ''<version>'' is the newest. | ||
| + | *** open the command line window: | ||
| + | **** move your mouse cursor over the window in which you saved the numpy[...].whl file | ||
| + | **** do a right mouse click while holding down the <code>SHIFT</code> key | ||
| + | **** in the menu select <code>Open command window here</code> | ||
| + | *** install numPy from command line and type: <code>c:\Python27\scripts\pip.exe install numpy-<version>-win_amd64.whl</code> | ||
| + | *** insert the correct version number for <code><version></code> | ||
| + | *** lxml (for Python 2.7 64 Bit): lxml is needed for reading mzML files with Python 2.7. [http://www.lfd.uci.edu/~gohlke/pythonlibs/#lxml Here] is a site where you can download it for your system. Please select ''lxml‑<version>‑cp27‑none‑win_amd64.whl'' | ||
| + | *** save it in the same folder as the numpy file | ||
| + | *** install lxml from command line: <code>c:\Python27\scripts\pip.exe install lxml-<version>-win_amd64.whl</code> | ||
| − | + | The requirements for Linux are the same. However, the links above are only for the Windows version. For Linux, please check out the repositories of your distribution. Further, the Python C extensions have to be build separately on Linux. Please contact me [mailto:herzog@mpi-cbg.de (Email)] for further information. | |
====Download link==== | ====Download link==== | ||
| Line 17: | Line 36: | ||
====Optional requirements==== | ====Optional requirements==== | ||
| + | |||
| + | =====File conversion===== | ||
LipidXplorer supports the generic file formats *.mzML and *.mzXML. Raw spectra as they are produced by the mass spectrometer have to be converted into one of those formats before they can be used with LipidXplorer. The recommended converter is [http://proteowizard.sourceforge.net/downloads.shtml MSConvert] from the ProteoWizard package. It supports the formats of the main mass spectrometer vendors and is maintained by a team of developers. I comes with an easy-to-use graphical user interface. | LipidXplorer supports the generic file formats *.mzML and *.mzXML. Raw spectra as they are produced by the mass spectrometer have to be converted into one of those formats before they can be used with LipidXplorer. The recommended converter is [http://proteowizard.sourceforge.net/downloads.shtml MSConvert] from the ProteoWizard package. It supports the formats of the main mass spectrometer vendors and is maintained by a team of developers. I comes with an easy-to-use graphical user interface. | ||
| + | ----- | ||
| − | + | '''[1]''' Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8. | |
| − | |||
Latest revision as of 17:05, 18 November 2016
Note: The current package of LipidXplorer is compatible with Microsoft Windows only. A Linux version has to be compiled first. This should be not a big problem. If anyone is interested, please write me.
Installation for Windows
LipidXplorer 32Bit
- Python 2.6 here !Note! Python version has to be >= 2.6.6
- wxPython 2.8 (for Python 2.6) here
- numPy (for Python 2.6) here
LipidXplorer 64Bit
- Python 2.7 here
- wxPython 2.8 (for Python 2.7) here
- install Python 2.7 and wxPython 2.8
- download the lipidxplorer third party dependencies here
- unzip it to a location of your choice
- double click on
install_dependencies.py - after the installation finished you can delete the unzipped folder - it is not needed any longer
- if this fails, you can manually install the dependencies:
- download
pip: get-pip.py - install
pipfrom cmd line withPython get-pip.py - download numPy (for Python 2.7 64Bit): Since Numpy is officially not supported for 64Bit there is an unofficial version here which can be used and installed. Please select numpy-<version>+mkl-cp27-none-win_amd64.whl where <version> is the newest.
- open the command line window:
- move your mouse cursor over the window in which you saved the numpy[...].whl file
- do a right mouse click while holding down the
SHIFTkey - in the menu select
Open command window here
- install numPy from command line and type:
c:\Python27\scripts\pip.exe install numpy-<version>-win_amd64.whl - insert the correct version number for
<version> - lxml (for Python 2.7 64 Bit): lxml is needed for reading mzML files with Python 2.7. Here is a site where you can download it for your system. Please select lxml‑<version>‑cp27‑none‑win_amd64.whl
- save it in the same folder as the numpy file
- install lxml from command line:
c:\Python27\scripts\pip.exe install lxml-<version>-win_amd64.whl
- download
The requirements for Linux are the same. However, the links above are only for the Windows version. For Linux, please check out the repositories of your distribution. Further, the Python C extensions have to be build separately on Linux. Please contact me (Email) for further information.
Download link
LipidXplorer can be downloaded here. Unzip it and store the folder at any place you prefer. LipidXplorer is started with a double click on "LipidXplorer.py". In the "mfql" folder you find example queries taken from the LipidXplorer paper[1].
Optional requirements
File conversion
LipidXplorer supports the generic file formats *.mzML and *.mzXML. Raw spectra as they are produced by the mass spectrometer have to be converted into one of those formats before they can be used with LipidXplorer. The recommended converter is MSConvert from the ProteoWizard package. It supports the formats of the main mass spectrometer vendors and is maintained by a team of developers. I comes with an easy-to-use graphical user interface.
[1] Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8.
