GATK: Difference between revisions

GATK (view source)

42 bytes removed , 3 years ago

clean up EN about Spark

Bureaucrats, cc_docs_admin, cc_staff

2,879

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-For the commands that do use spark, you can request multiple cpus. '''NOTE:''' please provide the exact number of cpus to the spark command, so if you requested 10 cpus, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to scale the spark calls with multinode SPARK cluster, you have to first [https://docs.computecanada.ca/wiki/Apache_Spark/en deploy an SPARK cluster] and then set up the appropriate variables in the GATK4 spark command.
+For the commands that do use Spark, you can request multiple cpus. '''NOTE:''' Please provide the exact number of cpus to the spark command.  For example if you requested 10 cpus, use <code>--spark-master local[10]</code> instead of <code>--spark-master local[*]</code>. If you want to use multiple nodes to scale the Spark cluster, you have to first [[Apache_Spark|deploy a SPARK cluster]] and then set the appropriate variables in the GATK command.
 ==Running GATK via Singularity== <!--T:36-->