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.img src/singularity_modules/pigz/2.4/pigz.def && \
-singularity sign bin/pigz:2.4.img

src/singularity_modules/pigz/2.4/pigz

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/pigz:2.4.img pigz $@

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.img src/singularity_modules/rsem/1.3.0/rsem.def && \
-singularity sign bin/rsem:1.3.0.img

src/singularity_modules/rsem/1.3.0/rsem

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/rsem:1.3.0.img rsem $@

src/singularity_modules/rsem/1.3.0/rsem.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-RSEM_VERSION=1.3.0
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="git \
-build-essential \
-ca-certificates \
-zlib1g-dev \
-bowtie2=${BOWTIE2_VERSION}* \
-samtools=${SAMTOOLS_VERSION}*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/deweylab/RSEM.git RSEM_${RSEM_VERSION} && \
-cd RSEM_${RSEM_VERSION} && \
-git checkout tags/v${RSEM_VERSION} && \
-make && \
-cd .. && \
-mv RSEM_${RSEM_VERSION}/rsem-* RSEM_${RSEM_VERSION}/rsem_* RSEM_${RSEM_VERSION}/convert-* RSEM_${RSEM_VERSION}/extract-* /usr/bin/ && \
-rm -Rf RSEM_${RSEM_VERSION}
-
-%environment
-export RSEM_VERSION=1.3.0
-export BOWTIE2_VERSION=2.3.4.1
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/salmon/0.8.2/build.sh

-#/bin/sh
-sudo singularity build --force bin/salmon:0.8.2.img src/singularity_modules/salmon/0.8.2/salmon.def && \
-singularity sign bin/salmon:0.8.2.img

src/singularity_modules/salmon/0.8.2/salmon

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/salmon:0.8.2.img salmon $@

src/singularity_modules/salmon/0.8.2/salmon.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-SALMON_VERSION=0.8.2
-PACKAGES="curl \
-ca-certificates"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L  https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz -o Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
-tar xzf Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && \
-mv Salmon-${SALMON_VERSION}_linux_x86_64/bin/* /usr/bin/ && \
-rm -Rf Salmon-${SALMON_VERSION}*
-
-%environment
-export SALMON_VERSION=0.8.2
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/sambamba/0.6.7/build.sh

-#/bin/sh
-sudo singularity build --force bin/sambamba:0.6.7.img src/singularity_modules/sambamba/0.6.7/sambamba.def && \
-singularity sign bin/sambamba:0.6.7.img

src/singularity_modules/sambamba/0.6.7/sambamba

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@

src/singularity_modules/sambamba/0.6.7/sambamba.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-SAMBAMBA_VERSION=0.6.7
-PACKAGES="curl=7.58.0* \
-ca-certificates=20180409 \
-build-essential=12.4* \
-zlib1g-dev=1:1.2.11*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
-mv sambamba /usr/bin/ && \
-rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
-
-%environment
-export SAMBAMBA_VERSION=0.6.7
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/samblaster/0.1.24/build.sh

-#/bin/sh
-sudo singularity build --force bin/samblaster:0.1.24.img src/singularity_modules/samblaster/0.1.24/samblaster.def && \
-singularity sign bin/samblaster:0.1.24.img

src/singularity_modules/samblaster/0.1.24/samblaster

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/samblaster:0.1.24.img samblaster $@

src/singularity_modules/samblaster/0.1.24/samblaster.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-SAMBLASTER_VERSION=0.1.24
-PACKAGES="curl \
-ca-certificates \
-build-essential \
-zlib1g-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
-cd samblaster-v.${SAMBLASTER_VERSION}/ && \
-make && \
-cp samblaster /usr/bin && \
-cd .. && \
-rm -R samblaster-v.${SAMBLASTER_VERSION}/
-
-%environment
-export SAMBLASTER_VERSION=0.1.24
-
-%runscript
-exec /bin/bash "$@"

src/singularity_modules/samtools/1.7/build.sh

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

src/singularity_modules/samtools/1.7/samtools

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

src/singularity_modules/sratoolkit/2.8.2/build.sh

-#/bin/sh
-sudo singularity build --force bin/sratoolkit:2.8.2.img src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def && \
-singularity sign bin/sratoolkit:2.8.2.img

src/singularity_modules/sratoolkit/2.8.2/sratoolkit

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/sratoolkit:2.8.2.img sratoolkit $@