From e5bd928904e2cab12e2ec95dc14699b04d7110c5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 29 Mar 2019 13:32:38 +0100
Subject: [PATCH] hisat2: add samtools to singularity modules
---
.../hisat2/2.0.0/hisat2.def | 40 ++++++++++++++-----
1 file changed, 29 insertions(+), 11 deletions(-)
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2.def b/src/singularity_modules/hisat2/2.0.0/hisat2.def
index a3941bf3..d9d77b68 100644
--- a/src/singularity_modules/hisat2/2.0.0/hisat2.def
+++ b/src/singularity_modules/hisat2/2.0.0/hisat2.def
@@ -1,21 +1,38 @@
Bootstrap: docker
-From: ubuntu:18.04
+From: alpine:3.8
%labels
-MAINTAINER Nicolas Fontrodona
+MAINTAINER Laurent Modolo
%post
+SAMTOOLS_VERSION=1.7
HISAT2_VERSION=2.0.0
-PACKAGES="unzip \
-gcc \
-g++ \
-make \
-curl \
-ca-certificates"
+PACKAGES="git \
+ make \
+ gcc \
+ musl-dev \
+ zlib-dev \
+ ncurses-dev \
+ bzip2-dev \
+ xz-dev \
+ bash \
+ curl \
+ zip \
+ g++ \
+ perl \
+ python"
+apk update && \
+apk add ${PACKAGES}
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
+git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION} && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
@@ -26,6 +43,7 @@ cp hisat2-* /usr/bin && \
rm -Rf hisat2-${HISAT2_VERSION}-beta
%environment
+export SAMTOOLS_VERSION=1.7
export HISAT2_VERSION=2.0.0
%runscript
--
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