music: fix containers and tests

src/docker_modules/music/6613c53/Dockerfile

-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 && \

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*

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

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 && \