From d752181f93034486b87549cefc40f7462122c8b5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 31 Mar 2020 14:36:29 +0200
Subject: [PATCH] Dockerfile: increase Xmx of java tools
---
src/.docker_modules/gatk/3.8.0/Dockerfile | 1 +
src/.docker_modules/picard/2.18.11/PicardCommandLine | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/.docker_modules/gatk/3.8.0/Dockerfile b/src/.docker_modules/gatk/3.8.0/Dockerfile
index 41d27614..2ef48edd 100644
--- a/src/.docker_modules/gatk/3.8.0/Dockerfile
+++ b/src/.docker_modules/gatk/3.8.0/Dockerfile
@@ -5,3 +5,4 @@ ENV GATK_VERSION=3.8.0
RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$@" > /bin/gatk3
RUN chmod +x /bin/gatk3
+RUN sed -i 's/java/java -Xmx40g/g' /bin/gatk3
diff --git a/src/.docker_modules/picard/2.18.11/PicardCommandLine b/src/.docker_modules/picard/2.18.11/PicardCommandLine
index 24e2d2ac..c8eebf83 100644
--- a/src/.docker_modules/picard/2.18.11/PicardCommandLine
+++ b/src/.docker_modules/picard/2.18.11/PicardCommandLine
@@ -12,4 +12,4 @@ PicardCommandLine)
;;
esac
-exec java -Xmx12g ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
+exec java -Xmx40g ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
--
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