Mirror of Apache Taverna Commandline (incubating)
APACHE-2.0 License
tl;dr: The Taverna code base is no longer maintained and is provided here for archival purposes.
From 2014 till 2020 this code base was maintained by the Apache Incubator project Apache Taverna (incubating) (see web archive and podling status).
In 2020 the Taverna community voted to retire Taverna as a project and withdraw the code base from the Apache Software Foundation.
This code base remains available under the Apache License 2.0
(see License below), but is now simply called
Taverna rather than Apache Taverna (incubating).
While the code base is no longer actively maintained, Pull Requests are welcome to the GitHub organization taverna, which may infrequently be considered by remaining volunteer caretakers.
Releases 2015-2018 during incubation at Apache Software Foundation are available from the ASF Download Archive https://archive.apache.org/dist/incubator/taverna/
Releases 2014 from the University of Manchester are on BitBucket https://bitbucket.org/taverna/
Releases 2009-2013 from myGrid are on LaunchPad https://launchpad.net/taverna/
Releases 2003-2009 are on SourceForge https://sourceforge.net/projects/taverna/files/taverna/
Binary JARs for Taverna are available from Maven Central https://repo.maven.apache.org/maven2/org/apache/taverna/ or the myGrid Maven repository https://repository.mygrid.org.uk/
Taverna Command-line Tool provides a shell command
for executing
Taverna workflows,
defined using either the Taverna Language
API in the
SCUFL2
.wfbundle
format, or in the .t2flow
format from
Taverna Workbench 2.5.
Workflow inputs can be provided as parameters or files, while outputs can be saved either to a folder or a Research Object bundle including detailed provenance, which can be inspected using Taverna Language's DataBundle support.
In addition to the Taverna Common Activities, the Command-line supports plugins using Taverna OSGi services.
Note that, except for command-line handling, this module relies on other Taverna components for the actual workflow execution.
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 contains any additional attributions and details about embedded third-party libraries and source code.
Taverna Command-line Tool product relies on other Taverna components which have their own source code repositories.
Any contributions received are assumed to be covered by the Apache License 2.0.
This code relies on other Taverna modules, which Maven should download automatically from Apache's Maven repository; however you might want to compile these yourself in the order below:
Please see the <properties>
of this pom.xml to find the
correct versions to build.
To build, use
mvn clean install
This will build each module and run its tests.
Note that this repository relies on
other 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.
If you are building on Windows, ensure you unpack this source code
to a folder with a short path name
lenght, e.g. C:\src
- as
Windows has a limitation on the total path length
which might otherwise
prevent this code from building successfully.
To skip the tests (these can be time-consuming), use:
mvn clean install -DskipTests
If you are modifying this source code independent of the 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 other -SNAPSHOT
Taverna dependencies.
If you are developing one of the
Taverna modules
and want to test it with the
Taverna Command-line Tool, make sure you build it
locally first with mvn clean install
to avoid downloading it from
the snapshot repository.
Then check that the the <properties>
section of the pom.xml
matches the <version>
of the module you are developing.
See also taverna-commandline-product/pom.xml
to hard-code versions of other dependencies.
The default SNAPSHOT update policy for mvn
is daily -
you can modify this behaviour with
--update-snapshots
or --no-snapshot-updates
To build a binary distribution 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.
After building, 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/
which contains the built Taverna Command-line Tool product.
If you prefer a ZIP file, then instead build with
the Maven -Prelease
option. You can then unzip at a location of
your choice.
If you are running on Windows you may need to
put Taverna Command-line Tool in a folder high in the
disk hierarchy (e.g. C:\Taverna
), this helps
avoid problems with Windows path-length restrictions.
Running executeworkflow.sh
(or executeworkflow.bat
) without arguments
will show the help:
$ ./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
contains a Hello World type example workflow in
SCUFL2 format.
$ ./executeworkflow.sh examples/helloworld.wfbundle
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!
On Windows:
C:\home\apache-taverna-commandline-3.1.0>executeworkflow.bat examples\helloworld.wfbundle
Outputs will be saved to the directory: C:\home\apache-taverna-commandline-3.1.0\Hello_World_output
Workflow completed.
C:\home\apache-taverna-commandline-3.1.0>type Hello_World_output\greeting
Hello, World!
This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software. BEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. See http://www.wassenaar.org/ for more information.
The U.S. Government Department of Commerce, Bureau of Industry and Security (BIS), has classified this software as Export Commodity Control Number (ECCN) 5D002.C.1, which includes information security software using or performing cryptographic functions with asymmetric algorithms. The form and manner of this Apache Software Foundation distribution makes it eligible for export under the License Exception ENC Technology Software Unrestricted (TSU) exception (see the BIS Export Administration Regulations, Section 740.13) for both object code and source code.
The following provides more details on the included cryptographic software:
lib
folder includes