Workflows

Dummy example of looping (3)

• Download

Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: Stian Soiland-Reyes

Hello abcd (1)

• Download

Example of using the same inserted nested workflow twice, iterating over it twice, which should mean 4 distinct calls to the inner "concatenate" process. This workflow is mainly useful for provenance testing purposes.

Created: 2016-03-15

Credits: Stian Soiland-Reyes

Extract DEC and RA from whitespace separat... (2)

• Download

This workflow extracts DEC and RA coordinates from a whitespace seperated file and this is a silly description.

Created: 2012-05-10 | Last updated: 2012-09-24

Credits: Stian Soiland-Reyes

Find workflow ancestors (2)

• Download

Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs).

Created: 2012-05-08 | Last updated: 2012-07-09

Credits: Stian Soiland-Reyes

Check Java Cryptography Unlimited Strength (1)

• Download

Checks if Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files is installed, and redirects user to correct download page and relevant lib/security folder if not.

Created: 2012-05-08 | Last updated: 2012-05-08

Credits: Stian Soiland-Reyes

Attributions: Find/show Taverna's home directory

Hello Anyone (1)

• Download

An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Attributions: Hello World

Hello World (1)

• Download

One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

XML-RPC example current time (1)

• Download

Using Apache ws-xmlrpc from Beanshell scripts to call time.xmlrpc.com - see http://www.xmlrpc.com/currentTime To use, download the JARs from http://ws.apache.org/xmlrpc/download.html (ie. http://apache.mirror.anlx.net//ws/xmlrpc/apache-xmlrpc-current-bin.zip ) - unzip and put into Taverna's home directory lib/ folder. Right-click on the Beanshell script and check the "Dependencies" tab to check that all JARs have been ticked off (minimum required: ws-common-util.jar, xmlrpc-client.jar and x...

Created: 2011-08-11 | Last updated: 2011-08-11

Credits: Stian Soiland-Reyes

Using a Create_List script with a dot-prod... (1)

• Download

Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

Created: 2011-02-02 | Last updated: 2011-02-02

Credits: Stian Soiland-Reyes

Biomart and 2x BLAST (1)

• Download

Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other.

Created: 2010-12-13 | Last updated: 2010-12-13