From 6d1694c12dcc811434367bef01c53ac51f2ddf9f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Sat, 6 Oct 2018 10:46:26 +0200
Subject: [PATCH] Bowtie2: add sambamba and samblaster to docker
---
src/docker_modules/Bowtie2/2.3.4.1/Dockerfile | 20 ++++++++++++++++++-
1 file changed, 19 insertions(+), 1 deletion(-)
diff --git a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile b/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
index 0f4ac75..ab3f2e0 100644
--- a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
+++ b/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:18.04
+FROM sambamba:0.6.7
MAINTAINER Laurent Modolo
ENV BOWTIE2_VERSION=2.3.4.1
@@ -10,3 +10,21 @@ ENV PACKAGES bowtie2=${BOWTIE2_VERSION}* \
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
+
+ENV PACKAGES curl=7.58.0* \
+ ca-certificates=20180409 \
+ build-essential=12.4* \
+ zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+ENV SAMBLASTER_VERSION=0.1.24
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${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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