KNIME nodes to configure, run and analyze PLANTS protein-ligand docking
PLANTS homepage at http://www.tcd.uni-konstanz.de/research/plants.php
This project uses Eclipse Tycho to perform build steps.
Included in PLANTS nodes plugin is the PLANTS executable with academic license (http://www.tcd.uni-konstanz.de/research/plants.php). When installing the plugin you have to accept this license agreement, you agree to use the included PLANTS executable only for academic usage. To use these nodes in a commercial manner you need to acquire a valid license yourself and configure the PLANTS node to use the commercial executable.
The PLANTS KNIME nodes themselves have the Apache 2.0 license.
Requirements:
Steps to get the PLANTS KNIME node inside KNIME:
https://3d-e-chem.github.io/updates/5.1
update site url.work with
pulldownThe examples/
folder contains example KNIME workflows.
mvn verify
An Eclipse update site will be made in p2/target/repository
directory.
The update site can be used to perform a local installation.
Steps to get development environment setup based on https://github.com/knime/knime-sdk-setup#sdk-setup:
KNIME Analytics Platform (5.1) - nl.esciencecenter.e3dchem.knime.plants.targetplatform/KNIME-AP-5.1.target
target definition.During import the Tycho Eclipse providers must be installed.
This plugin uses metanodes as it's public nodes. They are created in the following way:
examples/
directory.name
and customDescription
field inside examples/**/workflow.knime
is filled.plugin/src/knime/
directory.plugin/plugin.xml
as PersistedMetaNode in the org.knime.workbench.repository.metanode
extension.Tests for the node are in tests/src
directory.
Tests can be executed with mvn verify
, they will be run in a separate KNIME environment.
Test results will be written to test/target/surefire-reports
directory.
Code coverage reports (html+xml) can be found in the tests/target/jacoco/report/
directory.
There are no tests for the meta nodes as they are copied from the plugin to a workflow each time, which would make the test test itself.
Unit tests written in Junit4 format can be put in tests/src/java
.
See https://github.com/3D-e-Chem/knime-testflow#3-add-test-workflow
Running mvn commands can take a long time as Tycho fetches indices of all p2 update sites.
This can be skipped by running maven offline using mvn -o
.
mvn org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=<version>-SNAPSHOT
command.mvn package
, will create update site in p2/target/repository
mvn verify
mvn install -Dtarget.update.site=<path to update site>
is referenced by this upload
related identifier