From ba5a6bc73a64ce15a86776117246802e4d93abb6 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Mon, 24 Aug 2020 15:22:44 +0100
Subject: [PATCH] Removed gnomad datatarget from 2nd installation command.

---
 docs/Software_installation.md | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/docs/Software_installation.md b/docs/Software_installation.md
index 39c7dc4..13bd346 100644
--- a/docs/Software_installation.md
+++ b/docs/Software_installation.md
@@ -40,7 +40,20 @@ cd ../../genomes/Hsapiens/hg38/txtmp/
 mv variation/gnomad* ../variation/
 ```
 
-Now restart the installation as above.
+Now restart the installation without the gnomad datatarget.
+
+```
+cd /home/u035/project/software/install
+wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
+
+ulimit -n 4096
+
+python bcbio_nextgen_install.py /home/u035/project/software/bcbio \
+  --tooldir /home/u035/project/software/bcbio/tools \
+  --genomes hg38 --aligners bwa \
+  --datatarget variation \
+  --datatarget vep --datatarget dbnsfp --cores 32 &> bcbio_install_YYYYMMDDhhmm.log
+```
 
 Put a fake file name for genotype2phenotype field in genomes/hg38/seq/hg38-resources.yaml
 
-- 
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