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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 then create index pipeline which internally will be stored as a catalog job :
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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 :
| Code Block | ||
|---|---|---|
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/opt/opencga/bin/opencga-analysis.sh variant index --outdir /opt/opencga/sessions/jobs/J_2510 -DcalculateStats=true --annotate --file variantFile.vcf.gz --path tmp: ... |
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On startup, docker container will mount the locations listed in "dockerArgs" parameter in "configuration.yml" file 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) as described in index pipeline.
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