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Basic KGTK Installation

Installing KGTK

The following instructions install KGTK and the KGTK Jupyter Notebooks on Linux and MacOS systems.

If you want to install KGTK on a Microsoft Windows system, please
contact the KGTK team.

Our KGTK installations use a Conda virtual environment. If you don't have the Conda tools installed, follow this guide to install it. We recommend installing Miniconda installation rather than the full Anaconda installation.

Next, execute the following steps to install the latest stable release of KGTK:

conda create -n kgtk-env python=3.8
conda activate kgtk-env
conda install -c conda-forge graph-tool
conda install -c conda-forge jupyterlab
pip --no-cache install -U kgtk
python -m spacy download en_core_web_sm

You may sometimes need to install a specific release of KGTK, such as a prerelease that incorporates the latest changes. For example, if you need to install KGTK release 0.8.6b0, use the following pip command instead of the pip command shown above:

pip --no-cache install kgtk==0.8.6b0

If you encounter problems with your installation, or are interested in a detailed explanation of these commands, read more about the installation procedure here.

Running KGTK commands

To list all the available KGTK commands, run:

kgtk -h

To see the arguments of a particular KGTK command, run:

kgtk <command> -h

See our online documentation for additional suggestions.

Installing the KGTK Tutorial and Other Jupyter Notebooks

Choose a folder in which you want to install the KGTK Tutorial and other Jupyter notebooks. Change your current working directory to that foder.

cd /path/to/install/kgtk/tutorial

/path/to/install/kgtk/tutorial is an appropriate filesystem path of your choice.

Next, execute the following command:

git clone https://github.com/usc-isi-i2/kgtk-notebooks.git

This will create a new folder (kgtk-notebooks) in your existing folder, then download the KGTK Tutorial and other Jupyter notebook files into the new folder.

Change your current working directory to the kgtk-notebooks folder:

cd kgtk-notebooks

You are now in your kgtk-notebooks folder and ready to start the KGTK Tutorial using Jupyter Lab.

Running the KGTK Tutorial and Other Jupyter Notebooks

In your kgtk-notebooks folder, start the first KGTK Tutorial notebook using the following command:

jupyter lab part1-kgtk-intro.ipynb

This will start a Jupyter Lab notebook server in your current terminal session. Depending upon your system configuration, a Jupyter Lab interface will automatically open in one of your Web browser windows, or you can use the URI that the Jupyter Labs server prints to open a Jupyter Lab interface in your Web browser manually.

Resuming Work with KGTK in a New Terminal Session

If you have started a new terminal session and want to resume work with KGTK, first execute the following command in the new terminal session in order to activate your kgtk-env Conda virtual environment:

conda activate kgtk-env

You should now be able to execute KGTK commands on the command line.

If you want to start a new Jupiter Lab notebook server, activate your Conda virtual environment as shown above and then enter:

cd /path/to/install/kgtk/tutorial/kgtk-notebooks
jupyter lab

/path/to/install/kgtk/tutorial is the path you originally choose for installation of the KGTK Tutorial and other Jupyter notebooks.

Use the Jupyter Lab interface to select the KGTK Tutorial notebook on which you wish to resume work, or to select a new notebook to begin.

If you know the name of the notebook you want to start, you may put it on the end of the jupyter lab command line:

jupiter lab some-notebook-name.ipynb

Updating your KGTK installation

To get the latest stable release of the KGTK commands, execute the following commands:

conda activate kgtk-env
pip --no-cache install -U kgtk

To get the latest KGTK Jupyter notebooks, execute the following commands:

conda activate kgtk-env
cd /path/to/install/kgtk/tutorial/kgtk-notebooks
git pull

The conda activate kgtk-env commands shown above are not needed if you have already activated your kgtk-env Conda virtual environment in your current terminal session.