Getting started
Table of Contents
Instructions for getting SCKAN up and running.
The successful completion of the steps in this file should result in a window with welcome.org greeting you and giving you quick access to an interactive query interface.
SCKAN is distributed as two docker images.
- An image with the software needed to run queries tgbugs/musl:kg-release-user
- An image containing only the loaded databases tgbugs/sckan:latest
The underlying data and the tgbugs/sckan:latest image are also archived on Zenodo.
The latest data release can be obtained from https://doi.org/10.5281/zenodo.5337441.
Download Docker and X11
X11 configuration
linux
xhost local:docker
macos
open -a XQuartz # XXX Go to XQuartz > Preferences > Security # and enable Allow connections from network clients # you may need to restart XQuartz after this xhost +localhost
windows
& 'C:\Program Files\VcXsrv\vcxsrv.exe' -multiwindow -clipboard -wgl :0
Running
# obtain the latest release images from dockerhub docker pull tgbugs/musl:kg-release-user docker pull tgbugs/sckan:latest # create a container that can be used to mount the SCKAN data release as a volume docker create -v /var/lib/blazegraph -v /var/lib/scigraph --name sckan-data tgbugs/sckan:latest /bin/true # run the image ## linux docker run --volumes-from sckan-data -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY -it tgbugs/musl:kg-release-user ## macos docker run --volumes-from sckan-data -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=host.docker.internal:0 -it tgbugs/musl:kg-release-user ## windows docker run --volumes-from sckan-data -e DISPLAY=host.docker.internal:0 -it tgbugs/musl:kg-release-user
See the Mounting the sckan folder from the host section of the reference to run when mounting host folders to save your work.
If you update to a new version of tgbugs/sckan you will want to run
the following to update the sckan-data container.
docker rm sckan-data docker create -v /var/lib/blazegraph -v /var/lib/scigraph --name sckan-data tgbugs/sckan:latest /bin/true
Examples
Full workflows for various operating systems.
linux
Note that these commands assume >=docker-20 so make sure your
package index is up to date.
sudo apt install docker docker.io # ubuntu mint etc. sudo usermod -a -G docker ${USER} # you may need to get a new login shell at this point xhost local:docker docker pull tgbugs/musl:kg-release-user docker pull tgbugs/sckan:latest docker rm sckan-data docker create -v /var/lib/blazegraph -v /var/lib/scigraph --name sckan-data tgbugs/sckan:latest /bin/true docker run \ --volumes-from sckan-data \ -v /tmp/.X11-unix:/tmp/.X11-unix \ -e DISPLAY=$DISPLAY \ -it tgbugs/musl:kg-release-user
macos
Using https://brew.sh/.
brew install virtualbox xquartz brew install --cask docker open -a Docker # The docker command will not appear until you # go to Applications and run Docker and accept # the license agreements and grant permissions # there are some system level persmissions that # you will need to set for virtualbox open -a XQuartz # XXX Go to XQuartz > Preferences > Security # and enable Allow connections from network clients # you may need to restart XQuartz after this xhost +localhost docker pull tgbugs/musl:kg-release-user docker pull tgbugs/sckan:latest docker rm sckan-data docker create -v /var/lib/blazegraph -v /var/lib/scigraph --name sckan-data tgbugs/sckan:latest /bin/true docker run \ --volumes-from sckan-data \ -v /tmp/.X11-unix:/tmp/.X11-unix \ -e DISPLAY=host.docker.internal:0 \ -it tgbugs/musl:kg-release-user
windows
Using https://chocolatey.org/.
choco install wsl2 wsl-ubuntu-2004 vcxsrv docker-desktop docker & 'C:\Program Files\VcXsrv\vcxsrv.exe' -multiwindow -clipboard -wgl :0 docker pull tgbugs/musl:kg-release-user docker pull tgbugs/sckan:latest docker rm sckan-data docker create -v /var/lib/blazegraph -v /var/lib/scigraph --name sckan-data tgbugs/sckan:latest /bin/true docker run ` --volumes-from sckan-data ` -e DISPLAY=host.docker.internal:0 ` -it tgbugs/musl:kg-release-user
If you try to launch vcxsrv.exe more than once with the same display
number set you will encounter a fatal error.
Other ways to use the docker images
Beyond the interactive query interface, these docker images can be run as standalone SciGraph and Blazegraph instances of SCKAN for use in a variety of applications.
For example to run a specific release as a standalone endpoint you can run the following.
docker pull tgbugs/sckan:data-2022-03-19T001639Z docker create \ -v /var/lib/blazegraph \ -v /var/lib/scigraph \ --name sckan-data-2022-03-19 \ tgbugs/sckan:data-2022-03-19T001639Z \ /bin/true
docker run \ --detach \ --volumes-from sckan-data-2022-03-19 \ -p 9000:9000 \ -p 9999:9999 \ --entrypoint /etc/services.sh \ tgbugs/musl:kg-release-user
curl http://localhost:9000/scigraph/vocabulary/term/brain