From d667bfff50d2aae5c0ce3c99cc376dd7db040b70 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Fri, 13 Aug 2021 11:10:53 +0100
Subject: [PATCH] Update Software_installation_ultra2.md
---
docs/Software_installation_ultra2.md | 15 ++++++++++++---
1 file changed, 12 insertions(+), 3 deletions(-)
diff --git a/docs/Software_installation_ultra2.md b/docs/Software_installation_ultra2.md
index 19fe100..b5eb84a 100644
--- a/docs/Software_installation_ultra2.md
+++ b/docs/Software_installation_ultra2.md
@@ -1,4 +1,4 @@
-# Installation of software for trio whole exome project
+# Ultra2 - Installation of software for trio whole exome project
## Aspera
@@ -48,11 +48,20 @@ DATE=`date +%Y%m%d%H%M`
/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget vep &> bcbio_install_logs/bcbio_install_datatarget_vep_${DATE}.log
```
-gnomAD 3.1.1 installation will take about 6 days (old ultra). Might be faster on ultra2.
+We already had gnomAD 3.0 compiled and downloaded on the ultra2 bcbio installation, so this gets copied to `/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/variation`.
+
+```
+cd /home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/variation
+scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz ./
+scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz.csi ./
+scp ultra.epcc.ed.ac.uk:/home/u035/project/software/bcbio/genomes/Hsapiens/hg38/variation/gnomad_genome.vcf.gz.tbi ./
+```
+
+However, if needed, re-generate it like this. It took about 6 days on old ultra.
```
DATE=`date +%Y%m%d%H%M`
-/home/u035/project/software/bcbio/tools/bin/bcbio_nextgen.py upgrade -u skip --datatarget gnomad &> bcbio_install_logs/bcbio_install_datatarget_gnomad_${DATE}.log
+/home/u035/u035/shared/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