From ec1d865708ad7b16bf723805cb62d987a9a69b0f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Sat, 20 Feb 2021 08:21:14 +0100
Subject: [PATCH] docker: bwa replace sambamba with samtools
---
src/.docker_modules/bwa/0.7.17/Dockerfile | 19 ++++---------------
1 file changed, 4 insertions(+), 15 deletions(-)
diff --git a/src/.docker_modules/bwa/0.7.17/Dockerfile b/src/.docker_modules/bwa/0.7.17/Dockerfile
index eaae571b..b5b5859a 100644
--- a/src/.docker_modules/bwa/0.7.17/Dockerfile
+++ b/src/.docker_modules/bwa/0.7.17/Dockerfile
@@ -4,14 +4,11 @@ MAINTAINER Laurent Modolo
ENV BWA_VERSION=0.7.17
ENV SAMBLASTER_VERSION=0.1.24
-ENV PACKAGES curl=7.58* \
- ca-certificates=20180409 \
- build-essential=12.4* \
- zlib1g-dev=1:1.2.11*
+ENV PACKAGES curl \
+ g++
-RUN apt-get update && \
- apt-get install -y --no-install-recommends ${PACKAGES} && \
- apt-get clean
+RUN apk update && \
+ apk add ${PACKAGES}
RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
@@ -21,11 +18,3 @@ cp bwa /usr/bin && \
cd .. && \
rm -R bwa-${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}/
-RUN chmod +x /usr/bin/*
--
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