Monthly Archives: December 2012

SeqWare command

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MGI_12172012

java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.BundleManager -- --list-install
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.BundleManager --
--list-workflow-params --workflow-accession 7 > workflow.ini


java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher --  --ini-files workflow.ini  --workflow-accession 7 --schedule --parent-accession 24

java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.Metadata -- --list-tables
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.Metadata -- --table study --list-fields
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter -- -wa 7



nning Plugin: net.sourceforge.seqware.pipeline.plugins.BundleManager
Setting Up Plugin: net.sourceforge.seqware.pipeline.plugins.BundleManager@21f8c6df
=====================================================
===============INSTALLED WORKFLOWS===================
=====================================================
Name    Version Creation Date   SeqWare Accession       Bundle Location
-----------------------------------------------------
FileImport      0.1.0   Wed Jan 04 13:51:00 EST 2012    4       null
First           Fri Nov 30 16:17:31 EST 2012    15      null
HelloWorldWorkflow      1.0     Wed Aug 15 19:00:11 EDT 2012    7       /home/seqware/SeqWare/released-bundles/Workflow_Bundle_H
elloWorldWorkflow_1.0_SeqWare_0.12.5.zip