From 45be00ec6a1e4a28c7345066b5556cdce81f0d70 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 2 Oct 2018 13:51:33 +0200
Subject: [PATCH] BWA: add sambamba and samblaster to docker
---
src/docker_modules/BWA/0.7.17/Dockerfile | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/src/docker_modules/BWA/0.7.17/Dockerfile b/src/docker_modules/BWA/0.7.17/Dockerfile
index b218ba0..7a53849 100644
--- a/src/docker_modules/BWA/0.7.17/Dockerfile
+++ b/src/docker_modules/BWA/0.7.17/Dockerfile
@@ -1,7 +1,9 @@
-FROM ubuntu:18.04
+FROM sambamba:0.6.7
MAINTAINER Laurent Modolo
ENV BWA_VERSION=0.7.17
+ENV SAMBLASTER_VERSION=0.1.24
+
ENV PACKAGES curl=7.58.0* \
ca-certificates=20180409 \
build-essential=12.4* \
@@ -18,3 +20,11 @@ make && \
cp bwa /usr/bin && \
cd .. && \
rm -R bwa-${BWA_VERSION}/
+
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/
--
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