SeqWare/public-workflows — pull request #1 by briandoconnor (2014-03-17 05:27:32+00:00)
Title: Feature/brian bwa pancan gnos download

I think this is working. Sergei and/or Jonathan can you try it out on a fresh SeqWare-Vagrant 1.1 box on EBI? In order to test you need to get a .pem key from https://pancancer-token.annailabs.com/ and either put it's contents in workflow/scripts/gnostest.pem or change the setting in the workflow.ini file.

You can then build the workflow (on a SeqWare-Vagrant 1.1 VM) using:

mvn clean install

You can then launch the workflow using:

seqware bundle launch --dir target/Workflow_Bundle_BWA_2.0_SeqWare_1.0.11/

That just runs it with the bundled data (small test dataset from EBI), if you want to customize the ini you can do that and provide an ini file as an option.

I tried this whole process on a fresh SeqWare-Vagrant 1.1 VirtualBox VM using the config based on vagrant_cluster_launch.pancancer.seqware.install.sge_node.json.template. It worked fine.