GATK: Difference between revisions

GATK (view source)

30 bytes removed , 4 years ago

cc_staff

415

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 <pre>
 module load singularity
-singularity exec -B $PWD:/home -B /scratch/someuser:/outputs \
+singularity exec -B /home -B /project -B /scratch -B /localscratch <path to the image>/gatk.sif gatk [--java-options "-Xmx4G"] ToolName [GATK args]</pre>
-  -B /projects/someuser/path/to/inputs:/inputs <path to the image>/gatk {+options and arguments for running GATK}
-</pre>
 For more information about Singularity, you can watch the recorded [https://www.youtube.com/watch?v=kYb0aXS5DEE Singularity webinar].