GC2D
A visualisation and analysis tool for two dimensional chromatography data.
Features
- 1D, 2D and 3D representations of GCxGC data.
- Integration and convolution support.
- Importing of pre-formatted, comma separated GCxGC data.
Launching without installing
NOTE: Execution in the manner is heavily dependent on the python environment. Any changes to the source code, the python installation or the required dependencies could result in unexpected behavior.
Please ensure that you have python3 installed, you can get it from www.python.org. Also insure that you have installed the requirements. To do this, execute the following command from the project root directory in a terminal or cmd:
Windows: py -3 -m pip install -r requirements.txt
OSX/Linux: pip3 install -r requirements.txt
You can then execute your operating systems respective launch script.
Installation
Prerequisites
For all operating systems the installers require that you have installed:
- python3
- pip3 (This is usually installed with python3)
- git
All the scripts will check that you have the required programs. The Windows installer is capable of downloading and installing python3 for you, however it is highly recommended that you install it yourself.
NOTE: If you already have python3 installed, you may wish to setup a new environment before running the installer to avoid having all of GC2D's dependencies installed into your current environment. They will not be removed post installation.
NOTE: The installers can take quite some time to build GC-2D, especially on slower systems. Don't be worried if it
doesn't seem to be doing anything, particularly when it's Building PKG (CArchive) PKG-000.pkg.
Windows
Run the WINDOWS_INSTALL.bat. This will walk you through this installation and install
all required dependencies.
If python3 is not installed the installer can attempt to download and install python 3.7.3. Alternatively install it yourself from www.python.org. In theory, any version of python3 will work, however development and testing was done with python 3.7 so if at all possible use that version.
NOTE: If attempting to install on windows XP, you will need to manually install python 3.4. Newer versions of python3 cannot be installed on XP.
NOTE: If the python3 is installed by the installer, it will ask whether you wish to uninstall python3 afterwards.
Doing so will not completely remove python3. The python3 uninstaller will leave py installer.
This can be uninstalled from the ControlPanel -> Uninstall a Program.
NOTE: GC2D is installed to %LOCALAPPDATA%, and shortcuts are created in the start menu.
The registry is also edited. The uninstaller will completely remove these changes.
User configurations and preferences are saved in %APPDATA% and will NOT be removed by the uninstaller.
Troubleshooting
- If the installer fails to install python3, try installing it yourself from www.python.org.
- The Installer requires Internet access to install the dependencies for GC2D, if you need to run GC2D on an
un-networked PC, you can create a portable executable on another PC with
WINDOWS_CREATE_PORTABLE.batand transfer it. This will only work between the same Windows version and architecture.
OSX
If you don't already have python3 installed, install it from www.python.org, Python 3.7 is prefered, however any version of python3 will probably work.
Run OSX_INSTALL.command, either by starting it in a terminal, or by double clicking in Finder.
GC2D will now be installed as an App in your user Applications directory and it should be visible in launcher.
Linux/Other
NOTE: This may or may not work for you. We have found that praying to the mighty God of Linux, Linus Torvalds, will increase the chance of success. If you are familiar with pip, you may prefer the pip installation below.
For Linux and all other systems with a bash interpreter:
- Install python3 if it isn't installed already. Please refer to your distribution help documentation for how to do that.
- Run the
LINUX_INSTALL.shscript from the project directory. This will create a soft link called2D-GCto theLAUNCH_LINUX.shscript. You can then put this script anywhere on thePATHand it will be executable from the terminal.
Troubleshooting
The 2D-GC link is dependent on the current location of the 2D-GC source folder. If you move or delete this folder, the
link will no longer work.
Pip
An alternative is to install the application with Pip
- Install python3 and pip for python3 if those aren't installed already
- On the command line, go to the project root directory (the directory where setup.py and requirements.txt are located)
- Run
pip3 install --user -r requirements.txt - Run
pip3 install --user .(assuming that you're still in the same directory as setup.py) - To launch the project, run
python3 -m gc2d
NOTE: On mac OSX you need to install the latest pyqtgraph from github rather than from pip. There is a bug for HDPI screens that has been fixed in the later development versions but that is not yet included in the latest release.
If you install it in the order show here everything should work correctly, but if not you may need to uninstall pyqtgraph (pip3 uninstall pyqtgraph if it was installed through pip) and pip3 install --user -r requirements.txt again.
Uninstallation
Windows
Navigate to Control Panel -> Uninstall a Program and select GC2D like you would any other program.
This will remove the files from %LOCALAPPDATA%, the start menu shortcuts
and the GC2D entries in the registry. Desktop shortcuts will not be deleted.
Portable executables do not need uninstalling, just delete the executable.
OSX
Simply delete GC2D.app from your local Applications directory like you would any other app.
User preferences will not be removed. To also remove these delete the $HOME/.gc2d directory.
Linux/Other
Remove the 2D-GC link from your path.
User preferences can be found in $HOME/.gc2d, delete this folder to completely uninstall.
Pip
Run pip3 uninstall gc2d-rug.
This does not uninstall dependencies (pyqtgraph, numpy, etc.). To install dependencies use pip-autoremove.
TODO
- Uninstaller asks if user preferences/configurations should be deleted (100% removal).