diff --git a/src/docker_modules/music/6613c53/Dockerfile b/src/docker_modules/music/6613c53/Dockerfile index da153c729e5f5dec9584d6ceb58b5a61245cfb9c..aa47eb572ca48736457bb0f60b0857bbe6c5d9df 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 deea1fd3be8e9c032a417d90fb4255bf26dcc805..dcba024b879e8ef7720e35873d9e8101116891c6 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=${SAMTOOLS_VERSION}* \ ca-certificates=20180409 \ build-essential=12.4* \ zlib1g-dev=1:1.2.11* diff --git a/src/nf_modules/music/tests.sh b/src/nf_modules/music/tests.sh index 4cb3993905385e88bf6b71220bee875d8e080f82..4169c449d5706e01a28c443247bf04c2a39fe40d 100755 --- a/src/nf_modules/music/tests.sh +++ b/src/nf_modules/music/tests.sh @@ -7,3 +7,14 @@ cp data/tiny_dataset/map/tiny_v2.sort.bam data/tiny_dataset/map/tiny_v2_control. --index "data/tiny_dataset/map/*.sort.bam.bai*" \ --read_size 50 --frag_size 300 \ -resume + +if [ -x "$(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 fe9b6b1e18fa815ac7dc2739788dc08a1bef53ce..57a429047a561475ff170fdec4586fe4ccefbf57 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 && \