src/singularity_modules/gatk/4.0.8.1/gatk.def

-Bootstrap: docker
-From: broadinstitute/gatk:4.0.8.1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-
-GATK_VERSION=4.0.8.1
-cp gatk/gatk /usr/bin/
-
-%environment
-export GATK_VERSION=4.0.8.1
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/hisat2/2.0.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/hisat2:2.0.0.sif src/singularity_modules/hisat2/2.0.0/hisat2.def && \
-singularity sign bin/hisat2:2.0.0.sif

src/singularity_modules/hisat2/2.0.0/hisat2.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Nicolas Fontrodona
-
-%post
-HISAT2_VERSION=2.0.0
-PACKAGES="unzip \
-gcc \
-g++ \
-make \
-curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${HISAT2_VERSION}-beta-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
-unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
-cd hisat2-${HISAT2_VERSION}-beta && \
-make && \
-cp hisat2 /usr/bin && \
-cp hisat2-* /usr/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}-beta
-
-%environment
-export HISAT2_VERSION=2.0.0
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/htseq/0.8.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/htseq:0.8.0.sif src/singularity_modules/htseq/0.8.0/htseq.def && \
-singularity sign bin/htseq:0.8.0.sif

src/singularity_modules/htseq/0.8.0/htseq.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-HTSEQ_VERSION=0.8.0
-PACKAGES="build-essential \
-python3-pip \
-python3-setuptools \
-python3-dev \
-python3-wheel"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install numpy==1.14.3
-pip3 install pysam==0.15.0
-pip3 install HTSeq==${HTSEQ_VERSION}
-
-%environment
-export HTSEQ_VERSION=0.8.0
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/kallisto/0.43.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/kallisto:0.43.1.sif src/singularity_modules/kallisto/0.43.1/kallisto.def && \
-singularity sign bin/kallisto:0.43.1.sif

src/singularity_modules/kallisto/0.43.1/kallisto.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-KALLISTO_VERSION=0.43.1
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
-rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
-
-%environment
-export KALLISTO_VERSION=0.44.0
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/kallisto/0.44.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/kallisto:0.44.0.sif src/singularity_modules/kallisto/0.44.0/kallisto.def && \
-singularity sign bin/kallisto:0.44.0.sif

src/singularity_modules/kallisto/0.44.0/kallisto.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-KALLISTO_VERSION=0.44.0
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
-cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
-rm -Rf kallisto_linux-v${KALLISTO_VERSION}*
-
-%environment
-export KALLISTO_VERSION=0.44.0
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/macs2/2.1.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/bowtie/1.2.2/bowtie.def && \
-singularity sign bin/bowtie:1.2.2.sif

src/singularity_modules/multiqc/1.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/multiqc:1.0.sif src/singularity_modules/multiqc/1.0/multiqc.def && \
-singularity sign bin/multiqc:1.0.sif

src/singularity_modules/multiqc/1.0/multiqc.def

-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-MULTIQC_VERSION=1.0
-PACKAGES="build-essential \
-             python3-pip \
-             python3-setuptools \
-             python3-dev \
-             python3-wheel \
-             procps \
-             locales"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-locale-gen en_US.UTF-8
-LC_ALL=en_US.utf-8
-LANG=en_US.utf-8
-LC_ALL=C.UTF-8
-LANG=C.UTF-8
-
-pip3 install multiqc==${MULTIQC_VERSION}
-
-%environment
-export KALLISTO_VERSION=0.44.0
-export locale-gen en_US.UTF-8
-export LC_ALL=en_US.utf-8
-export LANG=en_US.utf-8
-export LC_ALL=C.UTF-8
-export LANG=C.UTF-8
-
-%runscript
-exec /bin/bash "$@"
-

src/singularity_modules/music/6613c53/build.sh

-#/bin/sh
-sudo singularity build --force bin/music:6613c53.sif src/singularity_modules/music/6613c53/music.def && \
-singularity sign bin/music:6613c53.sif

src/singularity_modules/music/6613c53/music.def

-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-MUSIC_VERSION=6613c53
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
-             make \
-             gcc \
-             musl-dev \
-             zlib-dev \
-             ncurses-dev \
-             bzip2-dev \
-             xz-dev \
-             ca-certificates \
-             bash"
-
-apk update && \
-apk add ${PACKAGES}
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/gersteinlab/MUSIC.git && \
-cd MUSIC && \
-git checkout ${MUSIC_VERSION} && \
-make clean && \
-make  && \
-cd .. && \
-mv MUSIC/bin/MUSIC /usr/bin/ && \
-mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
-mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
-rm -Rf MUSIC
-
-chmod +x /usr/bin/*
-
-%environment
-export MUSIC_VERSION=6613c53
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/picard/2.18.11/PicardCommandLine

-#!/bin/sh
-set -eu
-PRG="$(basename -- "$0")"
-case "$PRG" in
-picard-tools)
-        echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
-        ;;
-PicardCommandLine)
-        ;;
-*)
-        set -- "$PRG" "$@"
-        ;;
-esac
-
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"

src/singularity_modules/picard/2.18.11/build.sh

-#/bin/sh
-sudo singularity build --force bin/picard:2.18.11.sif src/singularity_modules/picard/2.18.11/picard.def && \
-singularity sign bin/picard:2.18.11.sif

src/singularity_modules/picard/2.18.11/picard.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%files
-src/singularity_modules/picard/2.18.11/PicardCommandLine /usr/bin/
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-PICARD_VERSION=2.18.11
-PACKAGES="default-jre \
-curl \
-ca-certificates"
-
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
-mkdir -p /usr/share/java/  && \
-mv picard.jar /usr/share/java/
-chmod +x /usr/bin/PicardCommandLine
-
-%environment
-export PICARD_VERSION=2.18.11
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/pigz/2.4/build.sh

-#/bin/sh
-sudo singularity build --force bin/pigz:2.4.sif src/singularity_modules/pigz/2.4/pigz.def && \
-singularity sign bin/pigz:2.4.sif

src/singularity_modules/pigz/2.4/pigz.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-PIGZ_VERSION=2.4
-PACKAGES=pigz=${PIGZ_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export PIGZ_VERSION=2.4
-export PACKAGES=pigz=${PIGZ_VERSION}*
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/rsem/1.3.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/rsem:1.3.0.sif src/singularity_modules/rsem/1.3.0/rsem.def && \
-singularity sign bin/rsem:1.3.0.sif