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

src/.singularity_modules/canu/1.6/canu.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CANU_VERSION=1.6
-PACKAGES=canu=${CANU_VERSION}*
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export CANU_VERSION=1.6
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/cutadapt/1.14/build.sh

-#/bin/sh
-sudo singularity build --force bin/cutadapt:1.14.img src/singularity_modules/cutadapt/1.14/cutadapt.def && \
-singularity sign bin/cutadapt:1.14.img

src/.singularity_modules/cutadapt/1.14/cutadapt

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:1.14.img cutadapt $@

src/.singularity_modules/cutadapt/1.14/cutadapt.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=1.14
-PACKAGES="bash \
-             python3 \
-             python3-dev \
-             musl-dev \
-             python3-pip \
-             gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=1.14
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/cutadapt/1.15/build.sh

-#/bin/sh
-sudo singularity build --force bin/cutadapt:1.15.img src/singularity_modules/cutadapt/1.15/cutadapt.def && \
-singularity sign bin/cutadapt:1.15.img

src/.singularity_modules/cutadapt/1.15/cutadapt

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:1.15.img cutadapt $@

src/.singularity_modules/cutadapt/1.15/cutadapt.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=1.15
-PACKAGES="bash \
-             python3 \
-             python3-dev \
-             musl-dev \
-             python3-pip \
-             gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=1.14
-
-%runscript
-exec /bin/bash "$@"
-xec /bin/bash "$@"

src/.singularity_modules/cutadapt/2.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/cutadapt:2.1.img src/singularity_modules/cutadapt/2.1/cutadapt.def && \
-singularity sign bin/cutadapt:2.1.img

src/.singularity_modules/cutadapt/2.1/cutadapt

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/cutadapt:2.1.img cutadapt $@

src/.singularity_modules/cutadapt/2.1/cutadapt.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-CUTADAPT_VERSION=2.1
-PACKAGES="bash \
-             python3 \
-             python3-dev \
-             musl-dev \
-             python3-pip \
-             gcc"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install setuptools
-pip3 install cutadapt==${CUTADAPT_VERSION}
-
-%environment
-export CUTADAPT_VERSION=2.1
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/deeptools/3.0.2/build.sh

-#/bin/sh
-sudo singularity build --force bin/deeptools:3.0.2.img src/singularity_modules/deeptools/3.0.2/deeptools.def && \
-singularity sign bin/deeptools:3.0.2.img

src/.singularity_modules/deeptools/3.0.2/deeptools

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/deeptools:3.0.2.img deeptools $@

src/.singularity_modules/deeptools/3.0.2/deeptools.def

-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-DEEPTOOLS_VERSION=3.0.2
-PACKAGES="build-essential \
-             python3-pip \
-             python3-setuptools \
-             python3-dev \
-             python3-wheel \
-             zlib1g-dev \
-             procps \
-             libcurl4-gnutls-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install deeptools==${DEEPTOOLS_VERSION}
-
-%environment
-export DEEPTOOLS_VERSION=3.0.2
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/deeptools/3.1.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/deeptools:3.1.1.img src/singularity_modules/deeptools/3.1.1/deeptools.def && \
-singularity sign bin/deeptools:3.1.1.img

src/.singularity_modules/deeptools/3.1.1/deeptools

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/deeptools:3.1.1.img deeptools $@

src/.singularity_modules/deeptools/3.1.1/deeptools.def

-Bootstrap: docker
-From: debian:stretch
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-DEEPTOOLS_VERSION=3.1.1
-PACKAGES="build-essential \
-             python3-pip \
-             python3-setuptools \
-             python3-dev \
-             python3-wheel \
-             zlib1g-dev \
-             procps \
-             libcurl4-gnutls-dev"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-pip3 install deeptools==${DEEPTOOLS_VERSION}
-
-%environment
-export DEEPTOOLS_VERSION=3.0.2
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/docker_to_singularity.sh

-# install spython
-# sudo pip3 install spython
-
-find src/docker_modules/ -name "Dockerfile" | \
-  perl -pe "s/docker/singularity/g" | \
-  perl -pe "s/Dockerfile//g" | \
-  awk '{system("mkdir -p " $0)}'
-
-find src/docker_modules/ -name "Dockerfile" | \
-  perl -pe "s/(^.*$)/spython recipe \1 > \1/g" | \
-  perl -pe "s/(^.*)docker_modules(.*$)/\1singularity_modules\2/g" | \
-  perl -pe "s/(^.*\/([^\/]*)\/[^\/]*\/)Dockerfile$/\1\2.def/g" | \
-  awk '{system($0)}'

src/.singularity_modules/fastp/0.19.7/build.sh

-#/bin/sh
-sudo singularity build --force bin/fastp:0.19.7.img src/singularity_modules/fastp/0.19.7/fastp.def && \
-singularity sign bin/fastp:0.19.7.img

src/.singularity_modules/fastp/0.19.7/fastp

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/fastp:0.19.7.img fastp $@

src/.singularity_modules/fastp/0.19.7/fastp.def

-Bootstrap: docker
-From: docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTP_VERSION=0.19.7
-
-%environment
-export FASTP_VERSION=0.19.7
-
-%runscript
-exec /bin/bash "$@"