src/.docker_modules/flexi_splitter/1.0.2/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/flexi_splitter:1.0.2
-docker build src/.docker_modules/flexi_splitter/1.0.2 -t 'lbmc/flexi_splitter:1.0.2'
-docker push lbmc/flexi_splitter:1.0.2
+# docker build src/.docker_modules/flexi_splitter/1.0.2 -t 'lbmc/flexi_splitter:1.0.2'
+# docker push lbmc/flexi_splitter:1.0.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/flexi_splitter:1.0.2" --push src/.docker_modules/flexi_splitter/1.0.2

src/.docker_modules/freebayes/1.3.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM quay.io/biocontainers/freebayes:1.3.2--py36h89e4507_1
 MAINTAINER Laurent Modolo

src/.docker_modules/freebayes/1.3.2/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/freebayes:1.3.2
-docker build src/.docker_modules/freebayes/1.3.2/ -t 'lbmc/freebayes:1.3.2'
-docker push lbmc/freebayes:1.3.2
+# docker build src/.docker_modules/freebayes/1.3.2/ -t 'lbmc/freebayes:1.3.2'
+# docker push lbmc/freebayes:1.3.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/freebayes:1.3.2" --push src/.docker_modules/freebayes/1.3.2

src/.docker_modules/g2gtools/0.2.7/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM jcrist/alpine-conda:4.6.8
 
 RUN /opt/conda/bin/conda config --add channels r \

src/.docker_modules/g2gtools/0.2.7/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/g2gtools:0.2.7
-docker build src/.docker_modules/g2gtools/0.2.7 -t 'lbmc/g2gtools:0.2.7'
-docker push lbmc/g2gtools:0.2.7
+# docker build src/.docker_modules/g2gtools/0.2.7 -t 'lbmc/g2gtools:0.2.7'
+# docker push lbmc/g2gtools:0.2.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/g2gtools:0.2.7" --push src/.docker_modules/g2gtools/0.2.7

src/.docker_modules/g2gtools/0.2.8/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 Laurent Modolo
 

src/.docker_modules/g2gtools/0.2.8/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/g2gtools:0.2.8
-docker build src/.docker_modules/g2gtools/0.2.8 -t 'lbmc/g2gtools:0.2.8'
-docker push lbmc/g2gtools:0.2.8
+# docker build src/.docker_modules/g2gtools/0.2.8 -t 'lbmc/g2gtools:0.2.8'
+# docker push lbmc/g2gtools:0.2.8
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/g2gtools:0.2.8" --push src/.docker_modules/g2gtools/0.2.8

src/.docker_modules/gatk/3.8.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM broadinstitute/gatk3:3.8-0
 MAINTAINER Laurent Modolo
 

src/.docker_modules/gatk/3.8.0/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/gatk:3.8.0
-docker build src/.docker_modules/gatk/3.8.0 -t 'lbmc/gatk:3.8.0'
-docker push lbmc/gatk:3.8.0
+# docker build src/.docker_modules/gatk/3.8.0 -t 'lbmc/gatk:3.8.0'
+# docker push lbmc/gatk:3.8.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/gatk:3.8.0" --push src/.docker_modules/gatk/3.8.0

src/.docker_modules/gatk/4.0.8.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM broadinstitute/gatk:4.0.8.1
 MAINTAINER Laurent Modolo
 

src/.docker_modules/gatk/4.0.8.1/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/gatk:4.0.8.1
-docker build src/.docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
-docker push lbmc/gatk:4.0.8.1
+# docker build src/.docker_modules/gatk/4.0.8.1 -t 'lbmc/gatk:4.0.8.1'
+# docker push lbmc/gatk:4.0.8.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/gatk:4.0.8.1" --push src/.docker_modules/gatk/4.0.8.1

src/.docker_modules/gffread/0.11.8/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM alpine:3.12
 MAINTAINER Laurent Modolo
 

src/.docker_modules/gffread/0.11.8/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/gffread:0.11.8
-docker build src/.docker_modules/gffread/0.11.8 -t 'lbmc/gffread:0.11.8'
-docker push lbmc/gffread:0.11.8
+# docker build src/.docker_modules/gffread/0.11.8 -t 'lbmc/gffread:0.11.8'
+# docker push lbmc/gffread:0.11.8
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/gffread:0.11.8" --push src/.docker_modules/gffread/0.11.8

src/.docker_modules/gffread/0.12.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM alpine:3.12
 MAINTAINER Laurent Modolo
 

src/.docker_modules/gffread/0.12.2/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/gffread:0.12.2
-docker build src/.docker_modules/gffread/0.12.2 -t 'lbmc/gffread:0.12.2'
-docker push lbmc/gffread:0.12.2
+# docker build src/.docker_modules/gffread/0.12.2 -t 'lbmc/gffread:0.12.2'
+# docker push lbmc/gffread:0.12.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/gffread:0.12.2" --push src/.docker_modules/gffread/0.12.2

src/.docker_modules/guppy-cpu/5.0.11/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+#Set the base image to Ubuntu 18.04
+FROM ubuntu:18.04
+
+# File Author / Maintainer
+MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
+
+ARG PACKAGE_VERSION=5.0.11
+ARG BUILD_PACKAGES="wget apt-transport-https"
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt update && \
+    apt install --yes $BUILD_PACKAGES && \
+    cd /tmp && \
+    wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~bionic_amd64.deb && \
+    apt install --yes /tmp/ont_guppy_cpu_${PACKAGE_VERSION}-1~bionic_amd64.deb && \
+    rm *.deb && \
+    apt-get autoremove --purge --yes && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
\ No newline at end of file

src/.docker_modules/guppy-cpu/5.0.11/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/guppy-cpu:5.0.11
+docker build src/.docker_modules/guppy-cpu/5.0.11 -t 'lbmc/guppy-cpu:5.0.11'
+docker push lbmc/guppy-cpu:5.0.11
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/guppy-cpu:5.0.11" --push src/.docker_modules/guppy-cpu/5.0.11
+

src/.docker_modules/guppy-cpu/6.0.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+#Set the base image to Ubuntu 18.04
+FROM ubuntu:18.04
+
+# File Author / Maintainer
+MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
+
+ARG PACKAGE_VERSION=6.0.1
+ARG BUILD_PACKAGES="wget apt-transport-https"
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt update && \
+    apt install --yes $BUILD_PACKAGES && \
+    cd /tmp && \
+    wget -q https://mirror.oxfordnanoportal.com/software/analysis/ont_guppy_cpu_${PACKAGE_VERSION}-1~bionic_amd64.deb && \
+    apt install --yes /tmp/ont_guppy_cpu_${PACKAGE_VERSION}-1~bionic_amd64.deb && \
+    rm *.deb && \
+    apt-get autoremove --purge --yes && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
\ No newline at end of file

src/.docker_modules/guppy-cpu/6.0.1/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/guppy-cpu:6.0.1
+docker build src/.docker_modules/guppy-cpu/6.0.1 -t 'lbmc/guppy-cpu:6.0.1'
+docker push lbmc/guppy-cpu:6.0.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/guppy-cpu:6.0.1" --push src/.docker_modules/guppy-cpu/6.0.1

src/.docker_modules/hicstuff/3.1.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM conda/miniconda3
+
+LABEL Name=hicstuff Version=3.1.3
+
+COPY hicstuff/* ./ /app/
+
+RUN apt-get update && apt-get install -y procps bash
+
+RUN apt update && apt install -y procps
+RUN conda update -y -n base -c defaults conda \
+&& conda init \
+&& conda config --add channels r \
+&& conda config --add channels defaults \
+&& conda config --add channels conda-forge \
+&& conda config --add channels bioconda \
+&& conda create -y -n hicstuff
+SHELL ["conda", "run", "-n", "hicstuff", "/bin/bash", "-c"]
+RUN conda install -c conda-forge -y \
+    pip \
+    bowtie2 \
+    minimap2 \
+    bwa \
+    samtools \
+    htslib \
+    pysam \ 
+    cooler \
+&& conda clean -afy \
+&& pip install -Ur requirements.txt \
+&& pip install . \
+&& chmod -R +x /usr/local/lib/python3.10/ \
+&& chmod -R +x /usr/local/lib/python3.10/lib-dynload/ \
+&& echo "conda activate hicstuff" >> /root/.bashrc
+
+ENV PATH /usr/local/envs/hicstuff/bin:/usr/local/condabin:$PATH