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Golr-Client Update to OWL-API 4.1.3 Jan 19, 2016
Lego Fix uber jars for command-line execution Jan 26, 2016
OWLTools-Annotation removing downloaded tmp file, and using different download method Apr 2, 2019
OWLTools-Core
OWLTools-NCBI delete out-dated assembly files Jan 26, 2016
OWLTools-Oort skip metadata in oort Feb 21, 2017
OWLTools-Parent Add back trove4j dependency. Dec 12, 2018
OWLTools-Runner Use -jar option to run from embedded jar. Possible fix for #256. Apr 24, 2019
OWLTools-Sim Reduce console output. Feb 25, 2019
OWLTools-Solr Fix some tests; disable many tests; at least have tests running. Feb 25, 2019
OWLTools-Web
docs as an official annotation_qc.xml is required for some things, but no … Mar 14, 2019
.gitignore using maven mojo to copy owltools resource into bin/ Mar 17, 2017
.travis.yml
LICENSE.txt update project url in pom and add license May 11, 2015
README.md updating readme for running owltools. Just copied from owltools. Sorr… Aug 17, 2017
build.sh Update build.sh Aug 19, 2015

README.md

Build Status DOI

For full documentation,

OWLTools Build Instructions

The OWLTools use maven as a build tool.

These instructions assume that a valid maven installation is available. The recommended maven version is 3.0.x, whereby x denotes the latest release for this branch.

Update: OWLTools also requires git. Only a proper clone via git, will allow the build to complete.

During the build process, we extract the git version and branch information. These details (and the build date) will be added to the manifest of the jar. If the .git folder is not available the build process will fail.

Building OWLTools

Prerequiste: Get source from Git

git clone https://github.com/owlcollab/owltools.git

Option 1: Command line

  1. Change into to the folder of OWLTools-Parent

2a) Run command: mvn clean install: This will trigger a complete build of all OWLTools projects and generate the required jars for execution. Remark: As part of the build the tests are executed. Any failed test will stop the build.

2b) Build without test execution (Not Recommended): Run command: mvn clean install -DskipTests

Option 2: Eclipse

Requires either:

  • Eclipse 3.7
  • Eclipse 3.6 with installed maven plugin m2e

Use the provided Eclipse launch configurations to trigger the build. The configuration are located in the OWLTools-Parent/eclipse-configs folder.

Downloading OWLTools

This option uses a pre-built JAR and script-wrapper instead of building owltools from the Java source. The JAR is built as part of the continuous building and test of the OWLTools project on a Jenkins server.

Go to http://build.berkeleybop.org/userContent/owltools/

Download owltools

Note: you may need to make this file executable. Occasionally when downloaded files lose the "executable" permisison. You can do this with chmod +x owltools.

If you add this to your PATH, you can run owltools on the command line:

export PATH=$PATH:directory/to/where/you/downloaded/owltools/
owltools -h

Running OWLTools (Unix and MacOS)

Running OWLTools requires a successful build, as described in the previous section.

  • OWLTools Command-Line Tools: The build produces a combined executable bash script and jar, to be found in OWLTools-Runner/bin or in the OWLTools-Runner/target directory

  • OORT: The executables and the generated jar are both located in OWLTools-Oort/bin

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