Commit ffebe272 authored by Nils Hoffmann's avatar Nils Hoffmann

Updated installation / distribution generation, README and setupLX.

parent eb8bfbb4
Copyright 2006-2010
Copyright 2006-2019
LipidXplorer 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
......
# -*- mode: python -*-
import os, sys, shutil
from zipfile import ZipFile
# copy assets to dist
assetsDir = "lx/stuff/"
if os.path.isdir("dist/lx/"):
shutil.rmtree("dist/lx/")
if os.path.isdir(DISTPATH+"/lx/"):
shutil.rmtree(DISTPATH+"/lx/")
shutil.copytree(assetsDir, "dist/lx/stuff/")
shutil.copytree(assetsDir, DISTPATH+"/lx/stuff/")
# copy mfql to dist
mfqlDir = "mfql/"
if os.path.isdir("dist/mfql/"):
shutil.rmtree("dist/mfql/")
if os.path.isdir(DISTPATH+"/mfql/"):
shutil.rmtree(DISTPATH+"/mfql/")
shutil.copytree(mfqlDir, "dist/mfql/")
shutil.copytree(mfqlDir, DISTPATH+"/mfql/")
shutil.copy("README.md", "dist/")
shutil.copy("README.md", DISTPATH+"/")
shutil.copy("CHANGELOG", DISTPATH+"/")
shutil.copy("COPYRIGHT.txt", DISTPATH+"/")
shutil.copy("LICENSES-third-party.txt", DISTPATH+"/")
block_cipher = None
......@@ -49,3 +53,12 @@ exe = EXE(pyz,
runtime_tmpdir=None,
icon='lx/stuff/lipidx_tb.ico',
console=False )
with ZipFile(DISTPATH+'.zip', 'w') as zipObj:
# Iterate over all the files in DISTPATH
for folderName, subfolders, filenames in os.walk(DISTPATH):
for filename in filenames:
#create complete filepath of file in directory
filePath = os.path.join(folderName, filename)
# Add file to zip
zipObj.write(filePath)
\ No newline at end of file
# LipidXplorer
LipidXplorer is a software that supports a variety of shotgun lipidomics experiments. It is designed to support bottom-up and top-down shotgun lipidomics experimenters performed at all type of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra.
LipidXplorer is a software that is designed to support bottom-up and top-down shotgun lipidomics experiments performed
on all types of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference
or simulated mass spectra but uses user-defined molecular fragment queries. It supports accurate, isotope-corrected
quantification based on the identified MS1 or MS2 level fragments.
## Downloading LipidXplorer
The latest (binary) release version of LipidXplorer is available from the [LIFS Portal](https://lifs.isas.de/lipidxplorer.html).
You can obtain the source code for LipidXplorer from our [GitLab server](https://gitlab.isas.de/lifs/lipidxplorer) and release version archives from [here](https://gitlab.isas.de/lifs/lipidxplorer/-/releases).
## Running LipidXplorer on Windows
For Windows, we provide a single executable for LipidXplorer. Go to the unzipped LipidXplorer directory and simply double-click on `LipidXplorer.exe` to start it.
For Windows, we provide a single executable for LipidXplorer for download from the [LIFS Portal](https://lifs.isas.de/lipidxplorer.html).
Please download the zip-archive to a location of your choice and extract (unzip) the contents.
Change to the unzipped LipidXplorer archive directory and simply double-click on `LipidXplorer.exe` to start it.
## Installation and Tutorials
Please see the installation instructions on our [Wiki](https://lifs.isas.de/wiki/index.php/LipidXplorer_Installation)
Please see more detailed installation instructions on our [Wiki](https://lifs.isas.de/wiki/index.php/LipidXplorer_Installation).
These also cover the case of working with the source code.
[The Wiki](https://lifs.isas.de/wiki/index.php) also offers an overview of the concepts behind LipidXplorer, as well as tutorial and reference materials.
## Working with the LipidXplorer Source Code
We recommend [PyCharm](https://www.jetbrains.com/pycharm/) for development of the LipidXplorer codebase and [Anaconda 3](https://www.anaconda.com/distribution/) to manage a stable, versioned Python environment.
Any other Python IDE will also work just as well.
Please see the `wx-py2.7-anaconda.yml` file in the project's source root folder for reference of an exported Anaconda environment. You can import it in your local Anaconda installation, call
conda env create -f wx-py2.7-anaconda.yml
## Creating a Windows Executable
We use pyinstaller to create a Python executable of LipidXplorer that can be easily run on Windows.
To create the exe in the dist folder, please run the following command:
We use `pyinstaller` (part of the Anaconda environment) to create a Python executable of LipidXplorer that can be easily run on Windows.
To create the exe in the `LipidXplorer-1.2.8` folder, please run the following command:
pyinstaller --distpath="LipidXplorer-1.2.8" LipidXplorer.spec
pyinstaller LipidXplorer.spec
This will also create a zip archive of the `distpath` folder in the root directory of the project: `LipidXplorer-1.2.8.zip`.
## Versioning
......
......@@ -14,5 +14,8 @@ setup(
"icon_resources": [(1, "lx/stuff/lipidx_ico.ico")]
}],
scripts = ['LipidXplorer.py'],
long_description = "..."
long_description = "LipidXplorer is a software that is designed to support bottom-up and top-down shotgun lipidomics experiments performed "+
"on all types of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference "+
"or simulated mass spectra but uses user-defined molecular fragment queries. It supports accurate, isotope-corrected "+
"quantification based on the identified MS1 or MS2 level fragments."
)
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