Running Taverna workflows n SSP

[Vladimir Korkhov]

Dear Noam,

I have some problems with running Taverna workflows on SSP.

I created a Taverna workflow (named HGNCEntrezKegggProfiler-Taverna) recently but it failed while executed. It seems that it needs to download something. In fact, these workflows normally need Taverna 2.5, Bioinformatics edition. Is it possible to install this version of Taverna? Maybe it will help to solve these errors. I also see the error "Execution failure, not data found": I wonder if any data is missing indeed.

I used another version of the workflow earlier (KeggPathwaysfromEnsembl) and it did not fail like this one.

Here is the log (stdout):

===

Taverna 2.4 starting time: Sun Dec  7 12:48:17 CET 2014

Looking for workflow engine files

Files extraction...Ended

Taverna 2.4 pre-installed workflow engine ver (10)

Running on: gb-wn01-emc.erasmusmc.nl

Execution by: uid=33392(vme047) gid=31620(vlemed) groups=31620(vlemed),30004(gina)

Executed command: ././executeTaverna2.sh New_HGNCEntrezKegggProfiler2.t2flow -inputfile genes gene_exp.diff gProfiler_Results genesandpaths pathwayImage

running /data/home/vme047/home_cream_408786360/CREAM408786360/auto-deploy-taverna/taverna-2.4.0/wfsubmit.sh New_HGNCEntrezKegggProfiler2.t2flow -inputfile genes gene_exp.diff gProfiler_Results genesandpaths pathwayImage

Submitting Workflow: New_HGNCEntrezKegggProfiler2.t2flow

ERROR 2014-12-07 12:48:42,540 (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Unable to determine host for:http://ws.zones.apache.org/repository2/org/helio/taverna/helio-activity/0.1/helio-activity-0.1.pom, maybe there is no network access?

WARN  2014-12-07 12:48:42,543 (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Ignoring repository http://ws.zones.apache.org/repository2/

...

WARN  2014-12-07 12:49:05,920 (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Socket error when connection tohttp://mirror.omii.ac.uk/maven/repository/

java.net.ConnectException: Connection refused

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351)

at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213)

...
WARN  2014-12-07 12:49:08,161 (net.sf.taverna.raven.repository.impl.LocalRepository:85) - Could not find artifact org.helio.taverna:helio-activity:0.1

net.sf.taverna.raven.repository.ArtifactNotFoundException: Could not find artifact org.helio.taverna:helio-activity:0.1: Can't find artifact for: org.helio.taverna:helio-activity:0.1

at net.sf.taverna.raven.repository.impl.LocalRepository.fetch(LocalRepository.java:820)

at net.sf.taverna.raven.repository.impl.LocalRepository.act(LocalRepository.java:537)

at net.sf.taverna.raven.repository.impl.LocalRepository.update(LocalRepository.java:491)

at net.sf.taverna.raven.plugins.PluginManager.addPlugin(PluginManager.java:222)

...
Getting files

Execution failure, not data found

Execution finished for Taverna 2.4

Taverna 2.4 ending time: Sun Dec  7 12:49:21 CET 2014

Execution done in: 64 seconds

===

Thanks, Vladimir

[Gabor Terstyanszky]

Hi Vladimir,

Currently, we are upgrading the Carmen cluster. I think it is the reason why you having this problem.

Noam, please manage this issue collaborating with Vladimir.

Gabor

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