Project

General

Profile

Edit History

Wiki » Release Checklist »

More about running fastq-to-gvcf » History » Version 1

Peter Amstutz, 04/07/2025 03:52 PM

1 1 Peter Amstutz 
h1. More about running bam-to-vcf
2 





    3
    
    
    
When we do releases, we run a test pipeline that is intended to be representative of a bioinformatics workload.





    4
    
    
    





    5
    
    
    
1. Deploy the version of @arvados-cwl-runner@ that you want to test and make sure that the corresponding @arvados/jobs@ image "has been built and uploaded to docker hub":https://ci.arvados.org/view/Release%20Pipeline/job/docker-jobs-image-release/ or built using the @arvados/build/build-dev-docker-jobs-image.sh@ script and uploaded using @arv-keepdocker@.





    6
    
    
    





    7
    
    
    
2. Clone https://git.arvados.org/arvados-tutorial.git/





    8
    
    
    





    9
    
    
    
3. Create an Arvados project for the test run





    10
    
    
    





    11
    
    
    
4. @cd arvados/tutorial/WGS-processing@





    12
    
    
    





    13
    
    
    
5. Run the following command: @arvados-cwl-runner --no-wait --disable-reuse --project-uuid <my project> cwl/wgs-processing-wf.cwl yml/wgs-processing-wf-chr19.yml@





    14
    
    
    





    15
    
    
    
6. Monitor this for success.  It usually takes about an hour to run.





    16
    
    
    





    17
    
    
    
If you are running this on @pirca@ then all the data should already be present.  If you are running it from somewhere else, you may need to do some additional data copying from @pirca@ to the other cluster.  The input document @yml/wgs-processing-wf-chr19.yml@ has the portable data hashes of the collections.