OWLTools
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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 Hardcoded the codes that check property mapping results Feb 15, 2018
OWLTools-Core Add option to avoid macro expansion when using species subsetter util. Dec 11, 2018
OWLTools-NCBI delete out-dated assembly files Jan 26, 2016
OWLTools-Oort skip metadata in oort Feb 21, 2017
OWLTools-Parent allow -P on merge-equivs Nov 10, 2017
OWLTools-Runner
OWLTools-Sim Fix uber jars for command-line execution Jan 26, 2016
OWLTools-Solr remove phylo_graph_json from solr loader; work on geneontology/amigo#542 Oct 4, 2018
OWLTools-Web More fixes for migration to OWL-API 4.1.3 Jan 22, 2016
docs/images for-docs Aug 21, 2015
.gitignore using maven mojo to copy owltools resource into bin/ Mar 17, 2017
.travis.yml Java 8 only Jan 22, 2016
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