Installing stand-alone GrapeTree¶
The stand-alone version emulates the EnteroBase version through a lightweight webserver running on your local computer. You will be interacting with the program as you would in EnteroBase; through a web browser. We recommend Google Chrome for best results. There are number of different ways to interact with GrapeTree, the easiest is to install via pip, or download the ready-built software here: https://github.com/achtman-lab/GrapeTree/releases
Installing and Running GrapeTree¶
Install via pip
pip install grapetree grapetree
For more information see: https://pypi.org/project/GrapeTree/
Running on Mac: Download GrapeTree_mac.zip
You will need to unzip GrapeTree_mac.zip (just double click). Inside there will be a directory. From this directory launch grapetree_mac. You may be warned about Security settings, if you right click on the grapetree_mac and then click “Open” it should be fine.
Running on Windows: Download GrapeTree_win.zip
Once downloaded, you will need to unzip GrapeTree_win.zip and then open the extracted folder and run GrapeTree_win.exe. When you run it the first time on windows you might get a prompt about security. On Windows 10, click the small text: “More info”, and then the button “Run Anyway”.
Running from Source code
EnteroMSTree - GrapeTree requires Python 2.7 and some additional python modules (listed in requirements.txt). The easiest way to install these modules is with pip:
pip install -r requirements.txt chmod +x binaries/
On Linux or MacOSX you need to make sure the binaries in binaries/ can be executed. To run GrapeTree;
- Navigate to the directory where you installed GrapeTree.
- Run it through python as below.
\GrapeTree>python main.py * Running on http://127.0.0.1:8000/ (Press CTRL+C to quit)
Running GrapeTree with no installation
If you just want to view and manipulate trees, without processing profile/FASTA files, it can simply be run by opening MSTree_holder.html in your web browser. It requires the ‘static folder’. This is essentially what happens if you visit https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
First look at GrapeTree¶
The program will automatically open your web browser and you will see the GrapeTree Splash Screen, as shown below.
If at anytime you want to restart the page you can visit http://localhost:8000 in your web browser, as shown below.
Let’s apply these concepts with data from a previously published study of Salmonella enterica serovar Agona. Click here for the first tutorial