is it possible to run this workflow using local path for genome.fa.gz?

Hi,

I am trying to run DEWrapperWorkflow locally. this is the output:

garvan@docker-host:~$ sudo docker run --rm -h master -it -v /var/run/docker.sock:/var/run/docker.sock \

                              -v /datastore:/datastore \
                              -v /home/garvan/workflow.ini:/workflow.ini \
                              -v /home/garvan/.ssh/gnos.pem:/home/garvan/.ssh/gnos.pem \
            pancancer/pcawg-dewrapper-workflow:1.0.7 \
              seqware bundle launch --dir /workflow/Workflow_Bundle_DEWrapperWorkflow_1.0.7_SeqWare_1.1.1 --engine whitestar --no-metadata --ini /workflow.ini
Performing launch of workflow 'DEWrapperWorkflow' version '1.0.7' [--plugin, net.sourceforge.seqware.pipeline.plugins.BundleManager, --, --install-dir-only, --bundle, /workflow/Workflow_Bundle_DEWrapperWorkflow_1.0.7_SeqWare_1.1.1, --out, /tmp/bundle_m anager3859287578986340414out] Installing Bundle (Working Directory Only) Bundle: /workflow/Workflow_Bundle_DEWrapperWorkflow_1.0.7_SeqWare_1.1.1 Added 'DEWrapperWorkflow' (SWID: 1) Bundle Has Been Installed to the MetaDB and Provisioned to /workflow/Workflow_Bundle_DEWrapperWorkflow_1.0.7_SeqWare_1.1.1! [--plugin, io.seqware.pipeline.plugins.WorkflowScheduler, --, --workflow-accession, 1, --host, master, --out, /tmp/scheduler7584673410809197826out, --i, /workflow.ini, --workflow-engine, whitestar, --no-meta-db, --] Created workflow run with SWID: 62 [--plugin, io.seqware.pipeline.plugins.WorkflowLauncher, --, --launch-scheduled, 62] [2016/07/14 01:00:54] | Number of submitted workflows: 1 Working Run: 62 Valid run by host check: 62 Launching via new launcher: 62 [SeqWare Pipeline] ERROR [2016/07/14 01:00:54] | You need to specify the output prefix for your workflow using either an override parameter at schedule-time or in your workflow INI file as output_prefix [SeqWare Pipeline] ERROR [2016/07/14 01:00:54] | You need to specify the output dir for your workflow using either an override parameter at schedule-time or in your workflow INI file as output_dir! WARNING Running in direct file mode, direct access BAM files will be used and assumed to be full paths

WARNING Running in local file upload mode, analyzed results files will be written to a local directory, you will need to upload to GNOS yourself

Using working directory: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449 [2016/07/14 01:00:54] | Row #0 , Attempt #1 out of 6 : s62_start_0 [2016/07/14 01:00:54] | Submitting 3000M batch with: s62_start_0 [2016/07/14 01:00:54] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_start_0-runner.sh [2016/07/14 01:00:55] | Workflow step succeeded: s62_start_0 [2016/07/14 01:00:55] | Row #1 , Attempt #1 out of 6 : s62_create_dirs_1 [2016/07/14 01:00:55] | Submitting 8192M batch with: s62_create_dirs_1 [2016/07/14 01:00:55] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_create_dirs_1-runner.sh [2016/07/14 01:00:55] | Workflow step succeeded: s62_create_dirs_1 [2016/07/14 01:00:55] | Row #2 , Attempt #1 out of 6 : s62_getEMBLDataFiles_2 [2016/07/14 01:00:55] | Submitting 8192M batch with: s62_getEMBLDataFiles_2 [2016/07/14 01:00:55] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getEMBLDataFiles_2-runner.sh [2016/07/14 01:00:55] | Workflow step succeeded: s62_getEMBLDataFiles_2 [2016/07/14 01:00:55] | Row #3 , Attempt #1 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:00:55] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:00:55] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:03:26] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:03:26] | Row #3 , Attempt #2 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:03:26] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:03:26] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:05:57] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:05:57] | Row #3 , Attempt #3 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:05:57] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:05:57] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:08:28] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:08:28] | Row #3 , Attempt #4 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:08:28] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:08:28] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:10:58] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:10:58] | Row #3 , Attempt #5 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:10:58] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:10:58] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:13:29] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:13:29] | Row #3 , Attempt #6 out of 6 : s62_getDKFZDataFiles_3 [2016/07/14 01:13:29] | Submitting 8192M batch with: s62_getDKFZDataFiles_3 [2016/07/14 01:13:29] | Running command: bash /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3-runner.sh [2016/07/14 01:16:00] | Workflow step failed: s62_getDKFZDataFiles_3 [2016/07/14 01:16:00] | Setting workflow-run status to failed for: 62 [--plugin, io.seqware.pipeline.plugins.WorkflowWatcher, --, --workflow-run-accession, 62] [SeqWare Pipeline] ERROR [2016/07/14 01:16:00] | You need to specify the output prefix for your workflow using either an override parameter at schedule-time or in your workflow INI file as output_prefix [SeqWare Pipeline] ERROR [2016/07/14 01:16:00] | You need to specify the output dir for your workflow using either an override parameter at schedule-time or in your workflow INI file as output_dir! WARNING Running in direct file mode, direct access BAM files will be used and assumed to be full paths

WARNING Running in local file upload mode, analyzed results files will be written to a local directory, you will need to upload to GNOS yourself

Workflow run 62 is currently failed [--plugin, net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker, --, --workflow-run-accession, 62] [2016/07/14 01:16:00] | Output for stdout due to workflow run failure:

Job Name: s62_start_0 Job ID: 458054854 File: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_start_0.o458054854 Updated: Thu Jul 14 01:00:55 UTC 2016 Contents Excerpt:

Full output: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_start_0.stdout

Job Name: s62_create_dirs_1 Job ID: 458055158 File: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_create_dirs_1.o458055158 Updated: Thu Jul 14 01:00:55 UTC 2016 Contents Excerpt:

Full output: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_create_dirs_1.stdout

Job Name: s62_getEMBLDataFiles_2 Job ID: 458055457 File: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getEMBLDataFiles_2.o458055457 Updated: Thu Jul 14 01:00:55 UTC 2016 Contents Excerpt:

Full output: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getEMBLDataFiles_2.stdout

Job Name: s62_getDKFZDataFiles_3 Job ID: 458055740 File: /datastore/oozie-b3b394b9-a818-4a0f-afd9-c8dafc41c449/generated-scripts/s62_getDKFZDataFiles_3.o458055740 Updated: Thu Jul 14 01:03:26 UTC 2016 Contents Excerpt: