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.
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
tool.wfbundle
Description: Binary data
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