From cc9f3d11d2bf8d66d3b9b7097b440a151a33b976 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 7 Mar 2019 11:35:54 +0100
Subject: [PATCH] music: fix containers and tests
---
src/docker_modules/music/6613c53/Dockerfile | 20 +++++++++++++++++--
.../samblaster/0.1.24/Dockerfile | 2 ++
src/nf_modules/music/tests.sh | 11 ++++++++++
.../music/6613c53/music.def | 11 +++++++---
4 files changed, 39 insertions(+), 5 deletions(-)
diff --git a/src/docker_modules/music/6613c53/Dockerfile b/src/docker_modules/music/6613c53/Dockerfile
index da153c72..aa47eb57 100644
--- a/src/docker_modules/music/6613c53/Dockerfile
+++ b/src/docker_modules/music/6613c53/Dockerfile
@@ -1,11 +1,27 @@
-FROM samtools:1.7
+FROM alpine:3.8
MAINTAINER Laurent Modolo
ENV MUSIC_VERSION=6613c53
-ENV PACKAGES g++
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES g++ \
+bash \
+pcre-dev \
+openssl-dev \
+build-base \
+bzip2-dev \
+xz-dev \
+git \
+curl
RUN apk update && \
apk add ${PACKAGES}
+RUN curl -L -o samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ http://jaist.dl.sourceforge.net/project/samtools/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && tar jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && cd samtools-${SAMTOOLS_VERSION}/ \
+ && ./configure --without-curses \
+ && make \
+ && make install
RUN git clone https://github.com/gersteinlab/MUSIC.git && \
cd MUSIC && \
diff --git a/src/docker_modules/samblaster/0.1.24/Dockerfile b/src/docker_modules/samblaster/0.1.24/Dockerfile
index deea1fd3..dcba024b 100644
--- a/src/docker_modules/samblaster/0.1.24/Dockerfile
+++ b/src/docker_modules/samblaster/0.1.24/Dockerfile
@@ -2,7 +2,9 @@ FROM ubuntu:18.04
MAINTAINER Laurent Modolo
ENV SAMBLASTER_VERSION=0.1.24
+ENV SAMTOOLS_VERSION=1.7
ENV PACKAGES curl=7.58.0* \
+ samtools=${SAMTOOLS_VERSION}* \
ca-certificates=20180409 \
build-essential=12.4* \
zlib1g-dev=1:1.2.11*
diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh
index 4cb39939..4169c449 100755
--- a/src/nf_modules/music/tests.sh
+++ b/src/nf_modules/music/tests.sh
@@ -7,3 +7,14 @@ cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control.
--index "data/tiny_dataset/map/*.sort.bam.bai*" \
--read_size 50 --frag_size 300 \
-resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/music/peak_calling_single.nf \
+ -c src/nf_modules/music/peak_calling_single.config \
+ -profile singularity \
+ --fasta "data/tiny_dataset/fasta/tiny_v2.fasta" \
+ --bam "data/tiny_dataset/map/*.sort.bam" \
+ --index "data/tiny_dataset/map/*.sort.bam.bai*" \
+ --read_size 50 --frag_size 300 \
+ -resume
+fi
diff --git a/src/singularity_modules/music/6613c53/music.def b/src/singularity_modules/music/6613c53/music.def
index fe9b6b1e..57a42904 100644
--- a/src/singularity_modules/music/6613c53/music.def
+++ b/src/singularity_modules/music/6613c53/music.def
@@ -10,6 +10,7 @@ SAMTOOLS_VERSION=1.7
PACKAGES="git \
make \
gcc \
+ g++ \
musl-dev \
zlib-dev \
ncurses-dev \
@@ -21,9 +22,13 @@ PACKAGES="git \
apk update && \
apk add ${PACKAGES}
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
+curl -L -o samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ http://jaist.dl.sourceforge.net/project/samtools/samtools/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && tar jxvf samtools-${SAMTOOLS_VERSION}.tar.bz2 \
+ && cd samtools-${SAMTOOLS_VERSION}/ \
+ && ./configure --without-curses \
+ && make \
+ && make install
git clone https://github.com/gersteinlab/MUSIC.git && \
cd MUSIC && \
--
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