src/singularity_modules/kallisto/0.43.1/kallisto

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/kallisto:0.43.1.img kallisto $@

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.img src/singularity_modules/kallisto/0.44.0/kallisto.def && \
-singularity sign bin/kallisto:0.44.0.img

src/singularity_modules/kallisto/0.44.0/kallisto

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/kallisto:0.44.0.img kallisto $@

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/macs2/2.1.2/build.sh

-#/bin/sh
-sudo singularity build --force bin/macs2:2.1.2.img docker://quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1 && \
-singularity sign bin/macs2:2.1.2.img

src/singularity_modules/macs2/2.1.2/macs2

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/macs2:2.1.2.img macs2 $@

src/singularity_modules/macs2/2.1.2/macs2.def

-Bootstrap: docker
-From: ubuntu:18.04
-%labels
-MAINTAINER Laurent Modolo
-%post
-
-MACS_VERSION=2.1.2
-PACKAGES="git \
-build-essential \
-python-pip \
-ca-certificates \
-python-setuptools \
-python-dev \
-python-numpy \
-python-wheel \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip install MACS2==${MACS_VERSION}
-
-%environment
-export MACS_VERSION=2.1.1.20160309
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/multiqc/1.0/build.sh

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

src/singularity_modules/multiqc/1.0/multiqc

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/multiqc:1.0.img multiqc $@

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/multiqc/1.7/build.sh

-#/bin/sh
-sudo singularity build --force bin/multiqc:1.7.img src/singularity_modules/multiqc/1.7/multiqc.def && \
-singularity sign bin/multiqc:1.7.img

src/singularity_modules/multiqc/1.7/multiqc

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/multiqc:1.7.img multiqc $@

src/singularity_modules/multiqc/1.7/multiqc.def

-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-MULTIQC_VERSION=1.7
-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.img src/singularity_modules/music/6613c53/music.def && \
-singularity sign bin/music:6613c53.img

src/singularity_modules/music/6613c53/music

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/music:6613c53.img music $@

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 \
-             g++ \
-             musl-dev \
-             zlib-dev \
-             ncurses-dev \
-             bzip2-dev \
-             xz-dev \
-             ca-certificates \
-             bash"
-
-apk update && \
-apk add ${PACKAGES}
-
-curl -L -o samtools-${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 && \
-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.img src/singularity_modules/picard/2.18.11/picard.def && \
-singularity sign bin/picard:2.18.11.img

src/singularity_modules/picard/2.18.11/picard

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/picard:2.18.11.img picard $@