diff --git a/docs/Software_installation.md b/docs/Software_installation.md index aa8d60224b4d17db8b59740c78d675cd7814d77f..b1eaba95bfdddd901cd42d0679cd0c6f4f724452 100644 --- a/docs/Software_installation.md +++ b/docs/Software_installation.md @@ -39,7 +39,12 @@ DATE=`date +%Y%m%d%H%M` /home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_datatarget_vep_${DATE}.log ``` -We already had gnomAD 3.0 compiled and downloaded from another bcbio installation, so this gets copied to /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation. +We already had gnomAD 3.0 compiled and downloaded from another bcbio installation, so this gets copied to /home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation. However, if needed, re-generate it like this. It will take about 6 days. + +``` +DATE=`date +%Y%m%d%H%M` +/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget gnomad &> bcbio_install_datatarget_gnomad_${DATE}.log +``` Increase JVM memory for GATK in galaxy/bcbio_system.yaml