singularity: remove module as they are pulled from docker since 0.4.0

src/.singularity_modules/bcftools/1.7/bcftools

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

src/.singularity_modules/bcftools/1.7/bcftools.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BCFTOOLS_VERSION=1.7
-PACKAGES=bcftools=${BCFTOOLS_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BCFTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/bcftools/1.7/build.sh

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

src/.singularity_modules/bedtools/2.25.0/bedtools

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bedtools:2.25.0.img bedtools $@

src/.singularity_modules/bedtools/2.25.0/bedtools.def

-Bootstrap: docker
-From: ubuntu:16.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BEDTOOLS_VERSION=2.25.0
-PACKAGES=bedtools=${BEDTOOLS_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BEDTOOLS_VERSION=2.25.0
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/bedtools/2.25.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/bedtools:2.25.0.img src/singularity_modules/bedtools/2.25.0/bedtools.def && \
-singularity sign bin/bedtools:2.25.0.img

src/.singularity_modules/bioawk/1.0/bioawk

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

src/.singularity_modules/bioawk/1.0/bioawk.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BIOAWK_VERSION=1.0
-PACKAGES="git \
-   build-essential \
-   ca-certificates \
-   zlib1g-dev \
-   byacc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/lh3/bioawk.git && \
-  cd bioawk && \
-  git checkout tags/v${BIOAWK_VERSION} && \
-  make && \
-  cd .. && \
-  mv bioawk/bioawk /usr/bin/ && \
-  rm -Rf bioawk
-
-%environment
-export BIOAWK_VERSION=1.0
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/bioawk/1.0/build.sh

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

src/.singularity_modules/bowtie/1.2.2/bowtie

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bowtie:1.2.2.img bowtie $@

src/.singularity_modules/bowtie/1.2.2/bowtie.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE_VERSION=1.2.2
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie=${BOWTIE_VERSION}* \
-samtools=${SAMTOOLS_VERSION}*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BOWTIE_VERSION=1.2.2
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/bowtie/1.2.2/build.sh

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

src/.singularity_modules/bowtie2/2.3.4.1/bowtie2

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bowtie2:2.3.4.1.img bowtie2 $@

src/.singularity_modules/bowtie2/2.3.4.1/bowtie2.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BOWTIE2_VERSION=2.3.4.1
-SAMTOOLS_VERSION=1.7
-PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
-samtools=${SAMTOOLS_VERSION}* \
-perl=5.26.1*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export BOWTIE2_VERSION=2.3.4.1
-export SAMTOOLS_VERSION=1.7
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/bowtie2/2.3.4.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/bowtie2:2.3.4.1.img src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
-singularity sign bin/bowtie2:2.3.4.1.img

src/.singularity_modules/bwa/0.7.17/build.sh

-#/bin/sh
-sudo singularity build --force bin/bwa:0.7.17.img src/singularity_modules/bwa/0.7.17/bwa.def && \
-singularity sign bin/bwa:0.7.17.img

src/.singularity_modules/bwa/0.7.17/bwa

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/bwa:0.7.17.img bwa $@

src/.singularity_modules/bwa/0.7.17/bwa.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-BWA_VERSION=0.7.17
-SAMBLASTER_VERSION=0.1.24
-
-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*
-
-curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
-tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
-cd bwa-${BWA_VERSION}/ && \
-make && \
-cp bwa /usr/bin && \
-cd .. && \
-rm -R bwa-${BWA_VERSION}/
-
-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 BWA_VERSION=0.7.17
-export SAMBLASTER_VERSION=0.1.24
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/canu/1.6/build.sh

-#/bin/sh
-sudo singularity build --force bin/canu:1.6.img src/singularity_modules/canu/1.6/canu.def && \
-singularity sign bin/canu:1.6.img

src/.singularity_modules/canu/1.6/canu

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/canu:1.6.img canu $@