LipidXplorer Installation - Revision history

Nils.hoffmann at 09:16, 11 March 2025

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Nils.hoffmann at 07:54, 13 September 2019

2019-09-13T07:54:03Z

Nils.hoffmann at 07:53, 13 September 2019

2019-09-13T07:53:48Z

Nils.hoffmann at 07:51, 13 September 2019

2019-09-13T07:51:01Z

Nils.hoffmann at 07:50, 13 September 2019

2019-09-13T07:50:24Z

Nils.hoffmann at 07:21, 13 September 2019

2019-09-13T07:21:59Z

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'''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 [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]
* 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====
LipidXplorer can be downloaded [https://sourceforge.net/projects/lipidxplorer/files/ 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 [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.

@@ Line 1: / Line 1: @@
-'''Note:''' The current package of LipidXplorer is mainly compatible with 64bit versions of '''Microsoft Windows''' (7,8,10) only. A Linux version is only available from source. If you need help, [https://lifs.isas.de/support please contact us].
+'''Note:''' The current package of LipidXplorer is mainly compatible with 64bit versions of '''Microsoft Windows''' (7,8,10) only. A Linux version is only available from source. If you need help, [https://lifs-tools.org/support please contact us].
 =====File conversion=====
@@ Line 8: / Line 8: @@
 ====Binary Distribution for Windows====
-The binary distribution of LipidXplorer is a zip-Archive containing the LipidXplorer.exe file. You can download the latest release version from [https://lifs.isas.de/lipidxplorer here]
+The binary distribution of LipidXplorer is a zip-Archive containing the LipidXplorer.exe file. You can download the latest release version from [https://github.com/lifs-tools/lipidxplorer.git here]
 Requirements:
@@ Line 30: / Line 30: @@
 * [https://repo.anaconda.com/archive/Anaconda2-2019.07-Windows-x86_64.exe Anaconda2, 64bit]
-The source code for LipidXplorer has been moved to the ISAS GitLab server. In order to clone it with TortoiseGit, follow these steps:
+The source code for LipidXplorer has been moved to the LIFS Tools GitHub. In order to clone it with TortoiseGit, follow these steps:
 # open a folder in your Windows Explorer where you want to keep the sourcecode locally,
 # right-click and select 'Git Clone...',
-# enter the repository URL: https://gitlab.isas.de/lifs-public/lipidxplorer.git ,
+# enter the repository URL: https://github.com/lifs-tools/lipidxplorer.git ,
 # left-click 'Ok'
@@ Line 50: / Line 50: @@
 If you use PyCharm as your IDE, the following instructions will help you get started:
-# Use https://gitlab.isas.de/lifs-public/lipidxplorer.git as the Git location: [https://www.jetbrains.com/help/pycharm/set-up-a-git-repository.html Set up the git repository]
+# Use https://github.com/lifs-tools/lipidxplorer.git as the Git location: [https://www.jetbrains.com/help/pycharm/set-up-a-git-repository.html Set up the git repository]
 # Use the wx-py27 anaconda environment and the conda Python 2.7 interpreter: [https://www.jetbrains.com/help/pycharm/conda-support-creating-conda-virtual-environment.html]
 # For further hints and tutorials, please see the [https://www.jetbrains.com/help/pycharm/quick-start-guide.html PyCharm Quickstart]

@@ Line 53: / Line 53: @@
 # Use the wx-py27 anaconda environment and the conda Python 2.7 interpreter: [https://www.jetbrains.com/help/pycharm/conda-support-creating-conda-virtual-environment.html]
 # For further hints and tutorials, please see the [https://www.jetbrains.com/help/pycharm/quick-start-guide.html PyCharm Quickstart]
 ----

← Older revision		Revision as of 07:53, 13 September 2019
Line 20:		Line 20:

	Please see the [[LipidXplorer Tutorial\|Tutorial]] for instructions on how to proceed.		Please see the [[LipidXplorer Tutorial\|Tutorial]] for instructions on how to proceed.
−

	====Sourcecode Installation for Windows====		====Sourcecode Installation for Windows====

@@ Line 8: / Line 8: @@
 ====Binary Distribution for Windows====
-The binary distribution of LipidXplorer is a zip-Archive containing the LipidXplorer.exe file. You can download the latest release version from [https://gitlab.isas.de/lifs-public/lipidxplorer/-/releases here]
+The binary distribution of LipidXplorer is a zip-Archive containing the LipidXplorer.exe file. You can download the latest release version from [https://lifs.isas.de/lipidxplorer here]
 Requirements:

@@ Line 31: / Line 31: @@
 * [https://repo.anaconda.com/archive/Anaconda2-2019.07-Windows-x86_64.exe Anaconda2, 64bit]
-The source code for LipidXplorer has been moved to the ISAS GitLab server. In order to check it out,
+The source code for LipidXplorer has been moved to the ISAS GitLab server. In order to clone it with TortoiseGit, follow these steps:
 # open a folder in your Windows Explorer where you want to keep the sourcecode locally,
@@ Line 40: / Line 40: @@
 The sourcecode should now be cloned into the selected directory within the 'lipidxplorer' folder.
 ----

@@ Line 1: / Line 1: @@
-'''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.
+'''Note:''' The current package of LipidXplorer is mainly compatible with 64bit versions of '''Microsoft Windows''' (7,8,10) only. A Linux version is only available from source. If you need help, [https://lifs.isas.de/support please contact us].
 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
@@ Line 30: / Line 76: @@
 *** 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.
+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 [https://lifs.isas.de/support contact us] for further information.
 -----
 '''[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.