From a482667b83340a241a24664f5c33b13dc5dfda38 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Thu, 27 Aug 2020 10:04:29 +0100
Subject: [PATCH] Notes on re-generating gnomaAD if needed.

---
 docs/Software_installation.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/docs/Software_installation.md b/docs/Software_installation.md
index aa8d602..b1eaba9 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
 
-- 
GitLab