Launcher for running Apache Taverna workflows.
Note that except for command line parsing, this module relies on other Apache Taverna modules for the actual workflow execution.
(c) 2007-2014 University of Manchester
(c) 2014-2015 Apache Software Foundation
This product includes software developed at The Apache Software Foundation.
Licensed under the Apache License 2.0, see the file LICENSE for details.
The file NOTICE contain any additional attributions and details about embedded third-party libraries and source code.
Please subscribe to and contact the [dev@taverna](http://taverna.incubator.apache.org/community/lists#dev mailing list) for any questions, suggestions and discussions about Apache Taverna.
Bugs and feature plannings are tracked in the Jira Issue tracker under the TAVERNA
component Taverna Commandline. Feel free to add an issue!
To suggest changes to this source code, feel free to raise a GitHub pull request. Any contributions received are assumed to be covered by the Apache License 2.0. We might ask you to sign a Contributor License Agreement before accepting a larger contribution.
Apache Taverna is an effort undergoing incubation at the Apache Software Foundation (ASF), sponsored by the Apache Incubator PMC.
Incubation is required of all newly accepted projects until a further review indicates that the infrastructure, communications, and decision making process have stabilized in a manner consistent with other successful ASF projects.
While incubation status is not necessarily a reflection of the completeness or stability of the code, it does indicate that the project has yet to be fully endorsed by the ASF.
To build, use
mvn clean install
This will build each module and run their tests.
Note that this repository relies on other Apache Taverna modules which will be downloaded from Maven repositories if they are not already present in the equivalent of your ~/.m2/repository
in the correct version.
To skip the tests (these can be time-consuming), use:
mvn clean install -DskipTests
If you are modifying this source code independent of the Apache Taverna project, you may not want to run the Rat Maven plugin that enforces Apache headers in every source file - to disable it, try:
mvn clean install -Drat.skip=true
If you are building a non-released version of this repository, (e.g. the pom.xml
declares a -SNAPSHOT
version), then Maven might download unreleased snapshot builds for internal -SNAPSHOT
Taverna dependencies.
If you want to avoid this, make sure you have built the corresponding Apache Taverna modules first. The default SNAPSHOT update policy for mvn
is daily - you can modify this behaviour with --update-snapshots
or --no-snapshot-updates
There is a nightly build of taverna-commandline-product using the -Pnighty
profile, which produces a downloadable taverna-command-line-product-3.1.0-incubating-SNAPSHOT-nightly.zip
- this
This should in theory contain all the needed dependencies (see lib/) and an executeworkflow.sh
/ executeworkflow.bat
that can run Taverna 3 workflows.
NOTE: These nightly builds should not be propagated beyond the dev@taverna community as they do not constitute an official Apache Release, and are provided only for development and testing purposes.
To build a released version as a distributable ZIP file that includes third-party dependencies as JAR files, build with the -Prelease
option, which would make taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-release.zip
or equivalent.
See the file target/maven-shared-archive-resources/META-INF/DEPENDENCIES
for details of the licenses of the third-party dependencies. All dependencies should be compatible with Apache License 2.0.
After building, see the taverna-commandline-product/target
directory. Inside you should find a folder like apache-taverna-commandline-3.1.0-incubating-SNAPSHOT-dev/
which contain the Apache Taverna Command Line product.
If you prefer a ZIP file, then build instead with the Maven options -Pnightly
or (for released versions) -Prelease
. You can then unzip at a location of your own choice.
$ ./executeworkflow.sh usage: executeworkflow [options] [workflow] -bundle <bundle> Save outputs to a new Workflow Run Bundle (zip). -clientserver Connect as a client to a derby server instance. -cmdir <directory path> Absolute path to a directory where Credential Manager's files (keystore and truststore) are located. ...
The folder examples
contain a Hello World type example workflow in SCUFL2 format.
$ ./executeworkflow.sh examples/helloworld.wfbundle Bundle: /tmp/robundle475236702008690452/robundle.zip Outputs will be saved to the directory: /home/johndoe/apache-taverna-commandline-3.1.0/Hello_World_output Workflow completed. $ cat Hello_World_output/greeting ; echo Hello, World!