Thank you very much indeed.
On 10/05/2012 12:14, Stian Soiland-Reyes wrote:
On Thu, May 3, 2012 at 10:33 AM, Dmitry<[email protected]> wrote:Is it possible o use SCUFL2 to execute plain executables (i.e. blast)? May this execution be distributed somehow on different nodes?Yes, just like in the Taverna 2 workbench, using the Tool activity. It can run the job locally, or on a set of SSH nodes. Support for grid submissions systems have not been finalized - Alan might have more details. Here's an example configuration (wfbundle attached): <Activity rdf:about="activity/wc/"> <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/tool"/> <name>wc</name> <inputActivityPort> <InputActivityPort rdf:about="activity/wc/in/in1"> <name>in1</name> <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer";>0</portDepth> </InputActivityPort> </inputActivityPort> <outputActivityPort> <OutputActivityPort rdf:about="activity/wc/out/STDOUT"> <name>STDOUT</name> <portDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer";>0</portDepth> <granularPortDepth rdf:datatype="http://www.w3.org/2001/XMLSchema#integer";>0</granularPortDepth> </OutputActivityPort> </outputActivityPort> </Activity> <Configuration rdf:about="configuration/wc/"> <rdf:type rdf:resource="http://ns.taverna.org.uk/2010/activity/tool#Config"/> <name>wc</name> <configure rdf:resource="activity/wc/"/> <mechanismName:mechanismName xmlns:mechanismName="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";>default local</mechanismName:mechanismName> <mechanismType:mechanismType xmlns:mechanismType="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType:mechanismType> <mechanismXML:mechanismXML xmlns:mechanismXML="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";><?xml version="1.0" encoding="UTF-8"?>
 <localInvocation />
 </mechanismXML:mechanismXML> <toolDescription:toolDescription xmlns:toolDescription="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";> <ToolDescription> <command>wc -l in1</command> <executionTimeoutInSeconds xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#int";>1800</executionTimeoutInSeconds> <includeStdErr xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>true</includeStdErr> <includeStdIn xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</includeStdIn> <includeStdOut xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>true</includeStdOut> <inputs> <InputMap> <input> <ScriptInput> <binary xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</binary> <charsetName>windows-1252</charsetName> <concatenate xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</concatenate> <file xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>true</file> <forceCopy xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</forceCopy> <list xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</list> <tag>in1</tag> <tempFile xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#boolean";>false</tempFile> </ScriptInput> </input> <port>in1</port> </InputMap> </inputs> <preparingTimeoutInSeconds xmlns:ns0="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; ns0:datatype="http://www.w3.org/2001/XMLSchema#int";>1200</preparingTimeoutInSeconds> <dc:description xmlns="http://purl.org/dc/elements/1.1/"/> <dc:title xmlns="http://purl.org/dc/elements/1.1/"/> </ToolDescription> </toolDescription:toolDescription> <toolId:toolId xmlns:toolId="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";>7e743ff3-103d-4343-b448-620a730a74c1</toolId:toolId> </Configuration> I must admit it is quite verbose and cryptic. This is due to the many different configuration options for the Tool activity in Taverna 2.x, and that I did not have time to finish 'tidying' the activity configuration when I did the Scufl2 translation. I don't understand many of the options in InputMap. This needs a bit of clean-up, which would require some work on the activity configuration in the Taverna 3 code base as well. For instance the mechanismXML and friends definitely have to go. Here's the SSH version: <mechanismName:mechanismName xmlns:mechanismName="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";>node1.example.com</mechanismName:mechanismName> <mechanismType:mechanismType xmlns:mechanismType="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType:mechanismType> <mechanismXML:mechanismXML xmlns:mechanismXML="http://ns.taverna.org.uk/2010/activity/tool#"; xmlns="http://ns.taverna.org.uk/2010/activity/tool#";><?xml version="1.0" encoding="UTF-8"?>
 <sshInvocation><sshNode><host>node1.example.com</host><port>22</port><directory>/tmp/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
 </mechanismXML:mechanismXML> I believe the tool activity did at some point support a list of SSH nodes - but I am unable to find how to do this now, as the GUI does not expose it. Alan might have more details. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ Developers Guide: http://www.taverna.org.uk/developers/
------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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