From: Tom Clegg <tom@tomclegg.ca>
Date: Tue, 10 Mar 2020 21:11:25 +0000 (-0400)
Subject: Update example script.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/b6183762d868bba50dc01baaaf90dbdd04805bcd

Update example script.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index ad87207921..6a18accc99 100755
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -7,12 +7,15 @@ go install
 lightning build-docker-image
 arv keep docker lightning-runtime
 
+priority=501
 project=su92l-j7d0g-jzei0m9yvgauhjf
+ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
 gvcf=su92l-4zz18-bgyq36m6gctk63q
 info=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
 tags=su92l-4zz18-92bx4zjg5hgs3yc
 
+genome=$(lightning ref2genome -project ${project} -priority ${priority} -ref ${ref_fa})
+fasta=$(lightning vcf2fasta   -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})
 unfiltered=$(
     lightning import       -project ${project} \
        -tag-library ${tags}/tagset.fa.gz \