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OpenCGA uses ARM template to auto deploy a pool with preconfigured opencga docker image. This pool is "AutoScale" enabled so will scale as number of variant index jobs will grow. These ARM script will also populate the following section in "configuration.yml"  which are enables OpenCGA daemon to submit job (azure task) to Azure Batch Service. Once an OpenGCA index job is created, it ll be prepared and then OpenCGA dameon will submit it to the Azure Batch Service for execution.

Configuration 

configuration.yml
....
execution:
  mode: AZURE
	...
  options:
    #Azure Batch Service information
    batchAccount : "batchAccount"
    batchKey : "batchKey"
    batchUri : "https://batchservice.uksouth.batch.azure.com"
    batchPoolId : "poolId"
    dockerImageName : "openCGADockerImageName" # preconfigured docker image
    dockerArgs : "dockerRunOptions"   # e,g; mount points etc.
....

Variant Index Job Creation

Once user create an OpenCGA variant indexing job, this will be stored in OpenCGA catalog. For example, following is an example to link a file in catalog and create index pipeline which internally will be stored as a catalog job :

OpenCGA Variant Index Job Creation
./opencga.sh files link -i ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -s "sudy" 
./opencga.sh variant index --file ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --calculate-stats --annotate -o tmp


If OpenCGA daemon is not running, user can start it with the following command:

OpenCGA Daemon
/opt/opencga/bin$ ./opencga-admin.sh catalog daemon --start <<< admin_password


Once daemon is running, it will fetch available jobs from the catalog, prepare them and then submit each catalog job as an "Azure Task" to the batch pool specified in "configuration.yml". A typical Azure task command will look like :

Azure Task Command
/opt/opencga/bin/opencga-analysis.sh variant index --outdir /opt/opencga/sessions/jobs/J_2510 --merge ADVANCED -DaggregatedType=NONE -DcalculateStats=true --annotate  -Dstdin=false -Dstdout=false --file ALL2.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz -DoverwriteAnnotations=false -Dsid=eyJkjGciOiJIUzI1NiJ9.eyJzdWIiOiJ0ZXN0IiwiYXVkIjoiT3BlbkNHQSB1c2VycyIsImlhdCI6MTU0Njk0OTM3NiwiZXhwIjoxNTQ2OTUyOTc2fQ.oRKCs0uUANRwZOp12NxbY3st6MVe9K1Wp3eMH1Bgjdc -Dinclude.extra-fields=all -DpostLoad.check.skip=false -Dload.split-data=false -Dexclude.genotypes=false --path tmp:


On startup, docker container will mount the locations listed in "dockerArgs"  parameter in "configuration.yml" file, e.g; "/opt/opencga/conf", "/opt/opencga/sessions", "storage location" (where variant files are stored) and any other run time options. This docker container will have access to shared configuration, session and storage location and will start indexing the variant file into storage ( HBase|MongoDB).


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