How to install gnomon

[Mac and Linux] Install gnomon using conda

Prerequisite: Install Conda

  • Make sure you have conda installed on your system. To check, simply open a new terminal window and type:

conda

  • If conda is installed, you should get a long return value describing how to use the command, otherwise you will get a command not found message.

  • If conda is not installed, we recommend that you install Miniconda by picking the latest installer suitable for your system.

About Conda and Miniconda

Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. Find out more on the official documentation

Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others.

Install Gnomon

Warning

Installing gnomon requires around 6 GB of free disk space.

  • Step 1: (Optional) Install Mamba in your (base) environment

conda install -n base -c conda-forge mamba

  • Step 2: Create a conda environment with the right python version. Then activate this environment

conda create -n gnomon python=3.9

conda activate gnomon

For Mac M1, you need to tell conda to use x86 architecture like this:

CONDA_SUBDIR=osx-64 conda create -n gnomon python=3.9
conda activate gnomon
conda config --env --set subdir osx-64

  • Step 3: Install gnomon and its dependencies

mamba install -c dtk-forge6 -c gnomon -c mosaic -c morpheme -c conda-forge gnomon

Note

At this stage the gnomon application is installed but it is “empty” since no plugins are installed by default. To actually make it usable, you will have to install plugin packages

  • Step 4: Install plugin packages for gnomon for instance:

gnomon-utils package install gnomon_package_tissueimagemesh

or alternatively:

mamba install -c gnomon -c dtk-forge6 -c conda-forge -c mosaic -c morpheme gnomon_package_tissueimagemesh

  • Step 5: Congrats, you can now launch the application

gnomon

Update gnomon

  • Step 1: Activate your (gnomon) environment

conda activate gnomon

  • Step 2: Update gnomon and its dependencies

gnomon-utils package update

or alternatively:

mamba update -c dtk-forge6 -c gnomon -c mosaic -c morpheme -c conda-forge gnomon

Finding existing plugin packages

You can find available packages by running the following command in your environment

gnomon-utils package search

[Windows] Install with Windows Subsystem for Linux (WSL)

Sources used for these instructions are:

1. Install the following dependencies

  1. WSL 2.

  2. Putty.

  3. VcXsrv, avalable on Source Forge.

2. Configure WSL

A $DISPLAY variable has to be defined to choose on which screen/computer to display. To configure it do this:

\> export DISPLAY=$(route.exe print | grep 0.0.0.0 | head -1 | awk '{print $4}'):0

Now, if you print $DISPLAY, you should see an IP followed by :0 such as:

> \> echo $DISPLAY
>
> \> 131.254.160.46:0

This IP is not constant and as to be set at each start of the WSL. You can tune your ~/.bashrc to set this variable at each WSL startup is you want.

Install awk is needed (for example on debian based distributions: sudo apt install awk ).

3. Configure X

VcXsrv

Once installed, launch XLauch and select options as shown below :

  1. Select display setting for windows. Then click Next.

  1. Clic on Next

  1. Tick Disable access control (Note: When it’s ticked, the X server VcXsrv is open to extern connections.). Clic on Next.

  1. Clic on Finish.

Putty & SSH

Start SSH service on WSL :

> \> sudo service ssh start

On WSL, type the command ip addr show eth0 and note the IP address. This step should be done at each start of WSL.

Launch Putty and configure the following parameters before connecting to WSL:

  1. Type the IP you just noted

  1. In the Menu SSH > X11, tick Enable X11 Forwarding.

  1. You can now start the session.

4. Launch gnomon

You can now launch gnomon through the WSL console:

gnomon