src/.docker_modules/deeptools/3.1.1/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 DEEPTOOLS_VERSION=3.1.1
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             libcurl4-gnutls-dev \
+             procps
+
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install deeptools==${DEEPTOOLS_VERSION}

src/.docker_modules/deeptools/3.1.1/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/deeptools:3.1.1
+# docker build src/.docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
+# docker push lbmc/deeptools:3.1.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.1.1" --push src/.docker_modules/deeptools/3.1.1

src/.docker_modules/deeptools/3.5.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.9-slim
+MAINTAINER Lauret Modolo
+
+ENV DEEPTOOLS_VERSION=3.5.0
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        libncurses5-dev \
+        procps
+RUN pip3 install deeptools==${DEEPTOOLS_VERSION}

src/.docker_modules/deeptools/3.5.0/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/deeptools:3.5.0
+# docker build src/.docker_modules/deeptools/3.5.0 -t 'lbmc/deeptools:3.5.0'
+# docker push lbmc/deeptools:3.5.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.5.0" --push src/.docker_modules/deeptools/3.5.0

src/.docker_modules/deeptools/3.5.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.8-slim
+MAINTAINER Lauret Modolo
+
+ENV DEEPTOOLS_VERSION=3.5.1
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        zlib1g-dev \
+        libbz2-dev \
+        liblzma-dev \
+        libcurl4-gnutls-dev \
+        libssl-dev \
+        libncurses5-dev \
+        libcurl4 \
+        libc6 \
+        procps
+RUN pip3 install pysam deeptools==${DEEPTOOLS_VERSION}

src/.docker_modules/deeptools/3.5.1/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/deeptools:3.5.1
+# docker build src/.docker_modules/deeptools/3.5.1 -t 'lbmc/deeptools:3.5.1'
+# docker push lbmc/deeptools:3.5.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.5.1" --push src/.docker_modules/deeptools/3.5.1

src/.docker_modules/docker_push.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+fd "Dockerfile" src/.docker_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'

src/.docker_modules/docker_update.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+fd "Dockerfile" src/.docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'

src/.docker_modules/emase-zero/0.3.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:buster as build
+MAINTAINER Laurent Modolo
+
+ENV EMASEZERO_VERSION=0.3.1
+ENV PACKAGES build-essential \
+    ca-certificates \
+    zlib1g-dev \
+    git
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN git clone https://github.com/churchill-lab/emase-zero.git \
+    && cd emase-zero/src/ \
+    && make \
+    && mv emase-zero /usr/local/bin/ \
+    && ldd /usr/local/bin/emase-zero
+# linux-vdso.so.1 (0x00007ffe8e35f000)
+# libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fbd358b5000)
+# libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fbd35731000)
+# libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fbd355ae000)
+# libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fbd35594000)
+# libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fbd353d3000)
+# /lib64/ld-linux-x86-64.so.2 (0x00007fbd35af7000)
+
+FROM debian:buster-slim
+
+COPY --from=build /usr/local/bin/emase-zero /usr/local/bin/
+COPY --from=build /lib/x86_64-linux-gnu/libz.so.1 /lib/x86_64-linux-gnu/
+COPY --from=build /lib/x86_64-linux-gnu/libm.so.6 /lib/x86_64-linux-gnu/
+COPY --from=build /lib/x86_64-linux-gnu/libgcc_s.so.1 /lib/x86_64-linux-gnu/
+
+RUN apt-get update && \
+    apt-get install -y procps bash

src/.docker_modules/emase-zero/0.3.1/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/emase-zero:0.3.1
+# docker build src/.docker_modules/emase-zero/0.3.1 -t 'lbmc/emase-zero:0.3.1'
+# docker push lbmc/emase-zero:0.3.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/emase-zero:0.3.1" --push src/.docker_modules/emase-zero/0.3.1

src/.docker_modules/emase/0.10.16/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM conda/miniconda2
+MAINTAINER Laurent Modolo
+
+ENV EMASE_VERSION=0.10.16
+RUN conda init \
+&& conda config --add channels r \
+&& conda config --add channels bioconda \
+&& conda create -y -n emase jupyter
+SHELL ["conda", "run", "-n", "emase", "/bin/bash", "-c"]
+RUN conda install -y -c kbchoi emase \
+&& echo "conda activate emase" >> /root/.bashrc
+RUN apt update && apt install -y procps
+
+ENV PATH /usr/local/envs/emase/bin:/usr/local/condabin:$PATH

src/.docker_modules/emase/0.10.16/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/emase:0.10.16
+# docker build src/.docker_modules/emase/0.10.16 -t 'lbmc/emase:0.10.16'
+# docker push lbmc/emase:0.10.16
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/emase:0.10.16" --push src/.docker_modules/emase/0.10.16

src/.docker_modules/fastp/0.19.7/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
+MAINTAINER Laurent Modolo

src/.docker_modules/fastp/0.19.7/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/fastp:0.19.7
+# docker build src/.docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
+# docker push lbmc/fastp:0.19.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.19.7" --push src/.docker_modules/fastp/0.19.7

src/.docker_modules/fastp/0.20.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/fastp:0.20.1--h8b12597_0
+MAINTAINER Laurent Modolo

src/.docker_modules/fastp/0.20.1/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/fastp:0.20.1
+# docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1'
+# docker push lbmc/fastp:0.20.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.20.1" --push src/.docker_modules/fastp/0.20.1

src/.docker_modules/fastp/0.23.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/fastp:0.23.2--hb7a2d85_2
+MAINTAINER Laurent Modolo

src/.docker_modules/fastp/0.23.2/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/fastp:0.23.2
+# docker build src/.docker_modules/fastp/0.23.2 -t 'lbmc/fastp:0.23.2'
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.23.2" --push src/.docker_modules/fastp/0.23.2
+docker push lbmc/fastp:0.23.2

src/docker_modules/FastQC/0.11.5/Dockerfile → src/.docker_modules/fastqc/0.11.5/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 FASTQC_VERSION=0.11.5
-ENV PACKAGES fastqc=${FASTQC_VERSION}*
+ENV PACKAGES fastqc=${FASTQC_VERSION}* \
+		perl=5.26*
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \

src/.docker_modules/fastqc/0.11.5/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/fastqc:0.11.5
+# docker build src/.docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
+# docker push lbmc/fastqc:0.11.5
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastqc:0.11.5" --push src/.docker_modules/fastqc/0.11.5