Squonk platform and computational notebook
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Alan Christie
Alan Christie - Updates readme
Latest commit 4dc5274 Nov 16, 2018

README.md

Squonk main repository

This is the main repository for Squonk, both the Squonk Platform and the Squonk Computational Notebook.

Currently the portal application part of the Squonk Computational Notebook is NOT included as that is in a separate repository that needs to be merged into this one. Also part of Squonk are components from the Pipelines repository.

The main source code is in the components directory. To build:

Checkout the pipelines project into the same directory that contains the squonk project. Then copy the current set of service descriptors to Squonk (this is needed for some of the tests and for those services to be present at runtime):

cd pipelines
./copy.dirs.sh

Next you need to setup access to the ChemAxon Maven repository. Instructions for this can be found here, though they are slightly garbled.

Create or edit the gradle.properties file in your $HOME/.gradle directory and add these 3 properties:

cxnMavenUser=YOUR_EMAIL
cxnMavenPassword=YOUR_ACCESS_KEY
cxnMavenRepositoryUrl=https://hub.chemaxon.com/artifactory/libs-release

Replace YOUR_EMAIL and YOUR_ACCESS_KEY with the appropriate values. Instructions for generating these can be found here

Now build squonk by moving into the squonk/components directory and use the Gradle build file there. e.g.

cd ../squonk/components
./gradlew build

For some of the tests and some of the RDKit services you will need RDKit with Java bindings to be present. See here for how to do this. If you don't have this then make sure the RDBASE environment variable is not set.

For the ChemAxon services and tests you will need a ChemAxon license file named license.cxl. Place this in your $HOME/.chemaxon directory AND in the docker/deploy/images/chemservices dir in the squonk distro.

If for these reasons you find some of the tests failing try using:

./gradlew build --continue

The deployment parts are found in the docker/deploy directory. NOTE: the deployment will be changing significantly over the coming months as we move to a Kubernetes/Opeshshift deployment.

Currently it is not expected that third party developers will find it easy to contribute to this codebase, but that will change. If you are interested in using or contributing contact Tim Dudgeon tdudgeon _at_ informaticsmatters _dot_ com.