From 1079c069dc0af322035dac788e25ccfb98eb188e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 29 Mar 2019 13:27:27 +0100
Subject: [PATCH] hisat2: add samtools to docker
---
src/docker_modules/hisat2/2.0.0/Dockerfile | 22 +++++++++-------------
1 file changed, 9 insertions(+), 13 deletions(-)
diff --git a/src/docker_modules/hisat2/2.0.0/Dockerfile b/src/docker_modules/hisat2/2.0.0/Dockerfile
index 04e439ff..640d6919 100644
--- a/src/docker_modules/hisat2/2.0.0/Dockerfile
+++ b/src/docker_modules/hisat2/2.0.0/Dockerfile
@@ -1,18 +1,15 @@
-FROM ubuntu:18.04
+FROM samtools:1.7
MAINTAINER Nicolas Fontrodona
ENV HISAT2_VERSION=2.0.0
-ENV PACKAGES unzip=6.0* \
- gcc=4:7.3.0* \
- g++=4:7.3.0* \
- make=4.1* \
- python \
- curl=7.58.0* \
- ca-certificates=20180409
+ENV PACKAGES curl \
+ zip \
+ g++ \
+ perl \
+ python
-RUN apt-get update && \
- apt-get install -y --no-install-recommends ${PACKAGES} && \
- apt-get clean
+RUN apk update && \
+ apk add ${PACKAGES}
RUN curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
@@ -20,5 +17,4 @@ cd hisat2-${HISAT2_VERSION}-beta && \
make && \
cp hisat2 /usr/bin && \
cp hisat2-* /usr/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}-beta
-
+rm -Rf hisat2-${HISAT2_VERSION}-beta
--
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