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;

  1. Navigate to the directory where you installed GrapeTree.
  2. 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.

https://bitbucket.org/repo/Xyayxn/images/2739749373-GrapeTree_start1.png

If at anytime you want to restart the page you can visit http://localhost:8000 in your web browser, as shown below.

https://bitbucket.org/repo/Xyayxn/images/1646166765-Grapetreestart2.png

Let’s apply these concepts with data from a previously published study of Salmonella enterica serovar Agona. Click here for the first tutorial