src/.docker_modules/macs3/3.0.0a6/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/macs3:3.0.0a6
+# docker build src/.docker_modules/macs3/3.0.0a6 -t 'lbmc/macs3:3.0.0a6'
+# docker push lbmc/macs3:3.0.0a6
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/macs3:3.0.0a6" --push src/.docker_modules/macs3/3.0.0a6

src/.docker_modules/minimap2/2.17/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools 
+# /usr/local/bin/samtools
+# / # ldd /usr/local/bin/samtools
+#         /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libncurses.so.6 => /usr/local/bin/../lib/libncurses.so.6 (0x7efddcfad000)
+#         libtinfo.so.6 => /usr/local/bin/../lib/libtinfo.so.6 (0x7efddcf6f000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7efddcf55000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+
+FROM quay.io/biocontainers/minimap2:2.17--hed695b0_3
+MAINTAINER Laurent Modolo
+ENV MINIMAP2_VERSION=2.17
+
+COPY --from=samtools /usr/local/bin/samtools /usr/local/bin/
+COPY --from=samtools /usr/local//lib/libncurses.so.6 /usr/local/lib/
+COPY --from=samtools /usr/local//lib/libtinfo.so.6 /usr/local/lib/
+
+# /usr/local/bin/minimap2
+# / # ldd /usr/local/bin/minimap2
+#         /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7fe14f7c4000)
+#         libpthread.so.0 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
\ No newline at end of file

src/.docker_modules/minimap2/2.17/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/minimap2:2.17
+# docker build src/.docker_modules/minimap2/2.17 -t 'lbmc/minimap2:2.17'
+# docker push lbmc/minimap2:2.17
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/minimap2:2.17" --push src/.docker_modules/minimap2/2.17

src/.docker_modules/minimap2/2.20/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools 
+# /usr/local/bin/samtools
+# / # ldd /usr/local/bin/samtools
+#         /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libncurses.so.6 => /usr/local/bin/../lib/libncurses.so.6 (0x7efddcfad000)
+#         libtinfo.so.6 => /usr/local/bin/../lib/libtinfo.so.6 (0x7efddcf6f000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7efddcf55000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+
+FROM quay.io/biocontainers/minimap2:2.20--h5bf99c6_0
+MAINTAINER adapted by Xavier Grand from Laurent Modolo template
+ENV MINIMAP2_VERSION=2.20
+
+COPY --from=samtools /usr/local/bin/samtools /usr/local/bin/
+COPY --from=samtools /usr/local//lib/libncurses.so.6 /usr/local/lib/
+COPY --from=samtools /usr/local//lib/libtinfo.so.6 /usr/local/lib/
+
+# /usr/local/bin/minimap2
+# / # ldd /usr/local/bin/minimap2
+#         /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7fe14f7c4000)
+#         libpthread.so.0 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
\ No newline at end of file

src/.docker_modules/minimap2/2.20/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/minimap2:2.20
+docker build src/.docker_modules/minimap2/2.20 -t 'lbmc/minimap2:2.20'
+docker push lbmc/minimap2:2.20
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/minimap2:2.20" --push src/.docker_modules/minimap2/2.20
\ No newline at end of file

src/.docker_modules/minimap2/2.24/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/samtools:0.1.18--hfb9b9cc_10 AS samtools 
+# /usr/local/bin/samtools
+# / # ldd /usr/local/bin/samtools
+#         /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libncurses.so.6 => /usr/local/bin/../lib/libncurses.so.6 (0x7efddcfad000)
+#         libtinfo.so.6 => /usr/local/bin/../lib/libtinfo.so.6 (0x7efddcf6f000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7efddcf55000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7efddcdcc000)
+
+FROM quay.io/biocontainers/minimap2:2.24--h7132678_1
+MAINTAINER adapted by Xavier Grand from Laurent Modolo template
+ENV MINIMAP2_VERSION=2.24
+
+COPY --from=samtools /usr/local/bin/samtools /usr/local/bin/
+COPY --from=samtools /usr/local//lib/libncurses.so.6 /usr/local/lib/
+COPY --from=samtools /usr/local//lib/libtinfo.so.6 /usr/local/lib/
+
+# /usr/local/bin/minimap2
+# / # ldd /usr/local/bin/minimap2
+#         /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libm.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x7fe14f7c4000)
+#         libpthread.so.0 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
+#         libc.so.6 => /lib64/ld-linux-x86-64.so.2 (0x7fe14f5a8000)
\ No newline at end of file

src/.docker_modules/minimap2/2.24/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/minimap2:2.24
+ docker build src/.docker_modules/minimap2/2.24 -t 'lbmc/minimap2:2.24'
+ docker push lbmc/minimap2:2.24
+ docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/minimap2:2.24" --push src/.docker_modules/minimap2/2.24
\ No newline at end of file

src/.docker_modules/multiqc/1.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.0
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+

src/.docker_modules/multiqc/1.0/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/multiqc:1.0
+# docker build src/.docker_modules/multiqc/1.0 -t 'lbmc/multiqc:1.0'
+# docker push lbmc/multiqc:1.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/multiqc:1.0" --push src/.docker_modules/multiqc/1.0

src/docker_modules/MultiQC/1.0/Dockerfile → src/.docker_modules/multiqc/1.11/Dockerfile

-FROM ubuntu:18.04
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.9-slim
 MAINTAINER Laurent Modolo
 
-ENV MULTIQC_VERSION=1.0
-ENV PACKAGES build-essential=12.4* \
-             python3-pip=9.0.1* \
-             python3-setuptools=39.0.1* \
-             python3-dev=3.6.5* \
-             python3-wheel=0.30.0*
+ENV MULTIQC_VERSION=1.11
+ENV PACKAGES procps locales
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \
     apt-get clean
 
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
 RUN pip3 install multiqc==${MULTIQC_VERSION}
+

src/.docker_modules/multiqc/1.11/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/multiqc:1.11
+# docker build src/.docker_modules/multiqc/1.11 -t 'lbmc/multiqc:1.11'
+# docker push lbmc/multiqc:1.11
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/multiqc:1.11" --push src/.docker_modules/multiqc/1.11

src/.docker_modules/multiqc/1.7/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.7
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+

src/.docker_modules/multiqc/1.7/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/multiqc:1.7
+# docker build src/.docker_modules/multiqc/1.7 -t 'lbmc/multiqc:1.7'
+# docker push lbmc/multiqc:1.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/multiqc:1.7" --push src/.docker_modules/multiqc/1.7

src/.docker_modules/multiqc/1.9/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.9
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             procps \
+             locales
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+

src/.docker_modules/multiqc/1.9/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/multiqc:1.9
+# docker build src/.docker_modules/multiqc/1.9 -t 'lbmc/multiqc:1.9'
+# docker push lbmc/multiqc:1.9
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/multiqc:1.9" --push src/.docker_modules/multiqc/1.9

src/.docker_modules/music/6613c53/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV MUSIC_VERSION=6613c53
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES g++ \
+bash \
+pcre-dev \
+openssl-dev \
+build-base \
+bzip2-dev \
+xz-dev \
+git \
+curl
+
+RUN apk update && \
+    apk add ${PACKAGES}
+RUN curl -L -o samtools-${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
+
+RUN 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
+
+RUN chmod +x /usr/bin/*
+

src/.docker_modules/music/6613c53/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/music:6613c53
+# docker build src/.docker_modules/music/6613c53 -t 'lbmc/music:6613c53'
+# docker push lbmc/music:6613c53
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/music:6613c53" --push src/.docker_modules/music/6613c53

src/.docker_modules/pandoc/2.11/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.13
+MAINTAINER Laurent Modolo
+
+ENV PANDOC_VERSION=2.11
+
+RUN echo "https://dl-cdn.alpinelinux.org/alpine/edge/testing" >> /etc/apk/repositories \
+  && apk update \
+  && apk add pandoc~=${PANDOC_VERSION} make

src/.docker_modules/pandoc/2.11/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/pandoc:2.11
+# docker build src/.docker_modules/pandoc/2.11 -t 'lbmc/pandoc:2.11'
+# docker push lbmc/pandoc:2.11
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/pandoc:2.11" --push src/.docker_modules/pandoc/2.11

src/.docker_modules/picard/2.18.11/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV PICARD_VERSION=2.18.11
+ENV PACKAGES default-jre=2:1.1* \
+    curl=7.58.0* \
+    ca-certificates=20180409
+
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \
+  mkdir -p /usr/share/java/  && \
+  mv picard.jar /usr/share/java/
+
+COPY PicardCommandLine /usr/bin/
+RUN chmod +x /usr/bin/PicardCommandLine