How to Run a Reference Pipeline using Local Input Files

Download & Install the Pipeline from NGC

Please refer to Setup section to install this Pipeline.

Note down the pipeline ID during the pipeline installation as it would be used in a later section to trigger a job with input files.

Trigger Pipeline

A pipeline can be triggered via Clara CLI. To trigger this pipeline, you will need to have a input folder (including sample.fasta and jobConfig) that can be used as source input data.

For this created pipeline, a sample input folder is available within the SDK in /input subfolder of the zipped test data file. Let's say that the path of the unzipped test data folder is TEST_DATA_FOLDER.

Open a terminal and go to the directory which contains the reference pipeline.

cd ~/.clara/pipelines/clara_denovo_assembly_pipeline

Trigger the pipeline (upload input files to Clara API Server) with the pipeline ID in the previous section.

clara create jobs -n denovo-test -p <pipeline ID> -f <TEST_DATA_FOLDER>

When the above step is completed, you should be able to see the following result in the terminal (UUID of Job and Payload may be different).

JOB ID:f3170b457f5c41879951e6da8f37341e
PAYLOAD ID:12bb398cb54844d5958d51e66e10713a

Note down this job ID and payload ID as they would be used in a later section to access output files.

Then, start the job:

clara start job -j <JOB ID>

Verify the Pipeline Execution in Dashboard

Go to the Clara dashboard UI using a web browser: The URL is: <IP of the machine>:8000
You should see a job with a name that includes the name of the job you specified (denovo-test)
You can inspect the status of each operator inside that job
Viewing status on a UI for Pipeline Jobs executed using the Clara orchestrator option is currently not available. See: orchestrator

Download and Verify the Outputs

Once the job has completed successfully,successfully, we can download output payload by using clara download command.

Output payload files are located under /operators/<operator name defined in the pipeline definition>/ folder. Since we triggered a pipeline whose genome sequence polish operator's name is racon, we can use the following command to download output files of racon operator into result folder:

clara download <Job ID>:/operators/racon/* result

Then, you can see the output files using the following command:

$ ls result

overlaps.paf          racon_polished_assembly_1.fa  racon_polished_assembly_4.fa
perf.yaml             racon_polished_assembly_2.fa  reads.fa
polished_assembly.fa  racon_polished_assembly_3.fa

If you are working with the server machine, the payload folder is directly accessible at the default payload folder /clara/payloads/<Payload ID>/.