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

src/.singularity_modules/fastqc/0.11.5/build.sh

-#/bin/sh
-sudo singularity build --force bin/fastqc:0.11.5.img src/singularity_modules/fastqc/0.11.5/fastqc.def && \
-singularity sign bin/fastqc:0.11.5.img

src/.singularity_modules/fastqc/0.11.5/fastqc

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/fastqc:0.11.5.img fastqc $@

src/.singularity_modules/fastqc/0.11.5/fastqc.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-FASTQC_VERSION=0.11.5
-PACKAGES="fastqc=${FASTQC_VERSION}* \
-perl=5.26*"
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-%environment
-export FASTQC_VERSION=0.11.5
-export PACKAGES=fastqc=${FASTQC_VERSION}*
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/file_handle/0.1.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/file_handle:0.1.1.img src/singularity_modules/file_handle/0.1.1/file_handle.def && \
-singularity sign bin/file_handle:0.1.1.img

src/.singularity_modules/file_handle/0.1.1/file_handle

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/file_handle:0.1.1.img file_handle $@

src/.singularity_modules/file_handle/0.1.1/file_handle.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-FILE_HANDLE_VERSION=0.1.1
-PACKAGES="git \
-ca-certificates "
-
-apt-get update && \
-apt-get install -y --no-install-recommends ${PACKAGES} && \
-apt-get clean
-
-git clone https://github.com/LBMC/file_handle.git && \
-cd file_handle && \
-git checkout tags/v${FILE_HANDLE_VERSION} && \
-cp src/file_handle.py /usr/bin/file_handle.py && \
-chmod +x /usr/bin/file_handle.py
-
-%environment
-export FILE_HANDLE_VERSION=0.1.1
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/gatk/4.0.8.1/build.sh

-#/bin/sh
-sudo singularity build --force bin/gatk:4.0.8.1.img src/singularity_modules/gatk/4.0.8.1/gatk.def && \
-singularity sign bin/gatk:4.0.8.1.img

src/.singularity_modules/gatk/4.0.8.1/gatk

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/gatk:4.0.8.1.img gatk $@

src/.singularity_modules/gatk/4.0.8.1/gatk.def

-Bootstrap: docker
-From: broadinstitute/gatk:4.0.8.1
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-
-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.img src/singularity_modules/hisat2/2.0.0/hisat2.def && \
-singularity sign bin/hisat2:2.0.0.img

src/.singularity_modules/hisat2/2.0.0/hisat2

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/hisat2:2.0.0.img hisat2 $@

src/.singularity_modules/hisat2/2.0.0/hisat2.def

-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMTOOLS_VERSION=1.7
-HISAT2_VERSION=2.0.0
-PACKAGES="git \
-          make \
-          gcc \
-          musl-dev \
-          zlib-dev \
-          ncurses-dev \
-          bzip2-dev \
-          xz-dev \
-          bash \
-          curl \
-          zip \
-          g++ \
-          perl \
-          python"
-apk update && \
-apk add ${PACKAGES}
-
-git clone https://github.com/samtools/htslib.git && \
-cd htslib && \
-git checkout ${SAMTOOLS_VERSION}  && \
-cd .. && \
-git clone https://github.com/samtools/samtools.git && \
-cd samtools && \
-git checkout ${SAMTOOLS_VERSION} && \
-make && \
-cp samtools /usr/bin/
-
-curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${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 SAMTOOLS_VERSION=1.7
-export HISAT2_VERSION=2.0.0
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/hisat2/2.1.0/build.sh

-#/bin/sh
-sudo singularity build --force bin/hisat2:2.1.0.img src/singularity_modules/hisat2/2.1.0/hisat2.def && \
-singularity sign bin/hisat2:2.1.0.img

src/.singularity_modules/hisat2/2.1.0/hisat2

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/hisat2:2.1.0.img hisat2 $@

src/.singularity_modules/hisat2/2.1.0/hisat2.def

-Bootstrap: docker
-From: alpine:3.8
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-SAMTOOLS_VERSION=1.7
-HISAT2_VERSION=2.1.0
-PACKAGES="git \
-          make \
-          gcc \
-          musl-dev \
-          zlib-dev \
-          ncurses-dev \
-          bzip2-dev \
-          xz-dev \
-          bash \
-          curl \
-          zip \
-          g++ \
-          perl \
-          python"
-apk update && \
-apk add ${PACKAGES}
-
-git clone https://github.com/samtools/htslib.git && \
-cd htslib && \
-git checkout ${SAMTOOLS_VERSION}  && \
-cd .. && \
-git clone https://github.com/samtools/samtools.git && \
-cd samtools && \
-git checkout ${SAMTOOLS_VERSION} && \
-make && \
-cp samtools /usr/bin/
-
-curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
-unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
-cd hisat2-${HISAT2_VERSION} && \
-make && \
-cp hisat2 /usr/bin && \
-cp hisat2-* /usr/bin && \
-rm -Rf hisat2-${HISAT2_VERSION}
-
-%environment
-export SAMTOOLS_VERSION=1.7
-export HISAT2_VERSION=2.1.0
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/htseq/0.11.2/build.sh

-#/bin/sh
-sudo singularity build --force bin/htseq:0.11.2.img src/singularity_modules/htseq/0.11.2/htseq.def && \
-singularity sign bin/htseq:0.11.2.img

src/.singularity_modules/htseq/0.11.2/htseq

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/htseq:0.11.2.img htseq $@

src/.singularity_modules/htseq/0.11.2/htseq.def

-Bootstrap: docker
-From: ubuntu:18.04
-
-%labels
-MAINTAINER Laurent Modolo
-
-%post
-mkdir -p /sps /pbs /scratch
-HTSEQ_VERSION=0.11.2
-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=0.11.2
-
-%runscript
-exec /bin/bash "$@"

src/.singularity_modules/htseq/0.8.0/build.sh

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

src/.singularity_modules/htseq/0.8.0/htseq

-#/bin/bash
-singularity exec /sps/lbmc/common/singularity/htseq:0.8.0.img htseq $@