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GATK: Difference between revisions
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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. 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. | 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 | ==Running GATK via Apptainer== <!--T:36--> | ||
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If you encounter errors like "[https://gatk.broadinstitute.org/hc/en-us/community/posts/360067054832-GATK-4-1-7-0-error-java-lang-IllegalArgumentException-malformed-input-off-17635906-length-1 IllegalArgumentException]" while using the installed modules on our clusters, we recommend you to try another workflow by using the program via [[ | If you encounter errors like "[https://gatk.broadinstitute.org/hc/en-us/community/posts/360067054832-GATK-4-1-7-0-error-java-lang-IllegalArgumentException-malformed-input-off-17635906-length-1 IllegalArgumentException]" while using the installed modules on our clusters, we recommend you to try another workflow by using the program via [[Apptainer]]. | ||
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A Docker image of GATK can be found [https://hub.docker.com/r/broadinstitute/gatk here] and other versions are available at this [https://hub.docker.com/r/broadinstitute/gatk/tags page]. You will need first to [[ | A Docker image of GATK can be found [https://hub.docker.com/r/broadinstitute/gatk here] and other versions are available at this [https://hub.docker.com/r/broadinstitute/gatk/tags page]. You will need first to [[Apptainer/en#Creating_an_image_using_Docker_Hub_and_Dockerfile|build an Apptainer image from the Docker image]]. | ||
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<pre> | <pre> | ||
module load | module load apptainer | ||
apptainer build gatk.sif docker://broadinstitute/gatk | |||
</pre> | </pre> | ||
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<pre> | <pre> | ||
module load | module load apptainer | ||
apptainer build gatk_VERSION.sif docker://broadinstitute/gatk:VERSION | |||
</pre> | </pre> | ||
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<pre> | <pre> | ||
module load | module load apptainer | ||
apptainer exec -B /home -B /project -B /scratch -B /localscratch \ | |||
<path to the image>/gatk.sif gatk [--java-options "-Xmx4G"] ToolName [GATK args]</pre> | <path to the image>/gatk.sif gatk [--java-options "-Xmx4G"] ToolName [GATK args]</pre> | ||
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For more information about | For more information about Apptainer, you can watch the recorded [https://www.youtube.com/watch?v=bpmrfVqBowY Apptainer webinar]. | ||
==Frequently asked questions == <!--T:23--> | ==Frequently asked questions == <!--T:23--> | ||