|
...
The workflows are downloaded from: https://github.com/gatk-workflows/gatk4-data-processing and https://github.com/gatk-workflows/gatk4-somatic-snvs-indels
Jumpstart
Here are the commands to test out the workflow using example data. The whole run needs a few hours if the cluster is not busy.
...
| Code Block |
|---|
# This will setup the path and environmental variables for the pipeline
module load gcc/6.2.0 python/2.7.12 rcbio/1.3.3
export PATH=/n/shared_db/singularity/hmsrc-gatk/bin:/home/ld32/rcbioDev/bin:$PATH
# setup database. Only need run this once. It will setup database in home, so make sure you have at least 5G free space at home.
setupDB.sh
|
...