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

src/.docker_modules/hicstuff/3.1.3/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/hicstuff:3.1.3
+docker build src/.docker_modules/hicstuff/3.1.3/ -t 'lbmc/hicstuff:3.1.3'
+docker push lbmc/hicstuff:3.1.3
+#docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/hicstuff:3.1.3" --push src/.docker_modules/hicstuff/3.1.3/

hicstuff @ c3d488f8

+Subproject commit c3d488f8012ed5296431ebf299a97f78d0b03407

src/.docker_modules/hisat2/2.0.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM lbmc/samtools:1.7
+MAINTAINER Nicolas Fontrodona
+
+ENV HISAT2_VERSION=2.0.0
+ENV PACKAGES curl \
+             zip \
+             g++ \
+             perl \
+             python
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN curl -k -L http://ccb.jhu.edu/software/hisat2/downloads/hisat2-${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

src/.docker_modules/hisat2/2.0.0/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/hisat2:2.0.0
+# docker build src/.docker_modules/hisat2/2.0.0 -t 'lbmc/hisat2:2.0.0'
+# docker push lbmc/hisat2:2.0.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/hisat2:2.0.0" --push src/.docker_modules/hisat2/2.0.0

src/.docker_modules/hisat2/2.1.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM lbmc/samtools:1.7
+MAINTAINER Nicolas Fontrodona
+
+ENV HISAT2_VERSION=2.1.0
+ENV PACKAGES curl \
+             zip \
+             g++ \
+             perl \
+             python
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${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}

src/.docker_modules/hisat2/2.1.0/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/hisat2:2.1.0
+# docker build src/.docker_modules/hisat2/2.1.0 -t 'lbmc/hisat2:2.1.0'
+# docker push lbmc/hisat2:2.1.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/hisat2:2.1.0" --push src/.docker_modules/hisat2/2.1.0

src/.docker_modules/hisat2/2.2.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM lbmc/samtools:1.14 as build
+
+ENV HISAT2_VERSION=2.2.1
+
+FROM quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3
+COPY --from=build \
+    /usr/local/bin/samtools /usr/local/bin/
+COPY --from=build \
+    /usr/local/bin/../lib/libhts.so.3 \
+    /usr/local/lib/libtinfow.so.6 \
+    /usr/local/lib/libncursesw.so.6 \
+    /usr/local/lib/libz.so.1 \
+    /usr/local/lib/libdeflate.so.0 \
+    /usr/local/lib/liblzma.so.5 \
+    /usr/local/lib/libbz2.so.1.0 /usr/local/lib/
+COPY --from=build \
+    /lib/x86_64-linux-gnu/libm.so.6 \
+    /lib/x86_64-linux-gnu/libpthread.so.0 \
+    /lib/x86_64-linux-gnu/libc.so.6 \
+    /lib/x86_64-linux-gnu/libdl.so.2 \
+    /lib/x86_64-linux-gnu/librt.so.1 /lib/x86_64-linux-gnu/
+COPY --from=build \
+    /lib64/ld-linux-x86-64.so.2 /lib64/
\ No newline at end of file

src/.docker_modules/hisat2/2.2.1/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/hisat2:2.2.1
+docker build src/.docker_modules/hisat2/2.2.1 -t 'lbmc/hisat2:2.2.1'
+docker push lbmc/hisat2:2.2.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/hisat2:2.2.1" --push src/.docker_modules/hisat2/2.2.1

src/.docker_modules/htseq/0.11.2/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 HTSEQ_VERSION=0.11.2
+ENV PACKAGES build-essential=12.4* \
+             python3-pip=9.0.1* \
+             python3-setuptools=39.0.1* \
+             python3-dev=3.6.7* \
+             python3-wheel=0.30.0*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install numpy==1.14.3
+RUN pip3 install pysam==0.15.0
+RUN pip3 install HTSeq==${HTSEQ_VERSION}

src/.docker_modules/htseq/0.11.2/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+# docker build src/docker_modules/HTSeq/0.11.2 -t 'htseq:0.11.2'

src/.docker_modules/htseq/0.13.5/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/htseq:0.13.5--py39h70b41aa_1
+MAINTAINER Laurent Modolo

src/.docker_modules/htseq/0.13.5/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/htseq:0.13.5
+docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5'
+docker push lbmc/htseq:0.13.5

src/.docker_modules/htseq/0.8.0/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 HTSEQ_VERSION=0.8.0
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install numpy==1.14.3
+RUN pip3 install pysam==0.15.0
+RUN pip3 install HTSeq==${HTSEQ_VERSION}

src/.docker_modules/htseq/0.8.0/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/htseq:0.8.0
+# docker build src/.docker_modules/htseq/0.8.0 -t 'lbmc/htseq:0.8.0'
+# docker push lbmc/htseq:0.8.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/htseq:0.8.0" --push src/.docker_modules/htseq/0.8.0

src/.docker_modules/htseq/1.99.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:20.04
+
+RUN apt-get update \
+    && apt-get install -y \
+     procps \
+     build-essential \
+     python3 \
+     python3-pip
+
+RUN pip install HTSeq==1.99.2

src/.docker_modules/htseq/1.99.2/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/htseq:1.99.2
+docker build src/.docker_modules/htseq/1.99.2 -t 'lbmc/htseq:1.99.2'
+docker push lbmc/htseq:1.99.2

src/.docker_modules/kallisto/0.43.1/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 KALLISTO_VERSION=0.43.1
+ENV PACKAGES curl=7.58.0* \
+   ca-certificates=20180409
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L  https://github.com/pachterlab/kallisto/releases/download/v${KALLISTO_VERSION}/kallisto_linux-v${KALLISTO_VERSION}.tar.gz -o kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
+cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
+rm -Rf kallisto_linux-v${KALLISTO_VERSION}*

src/.docker_modules/kallisto/0.43.1/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/kallisto:0.43.1
+# docker build src/.docker_modules/kallisto/0.43.1 -t 'lbmc/kallisto:0.43.1'
+# docker push lbmc/kallisto:0.43.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kallisto:0.43.1" --push src/.docker_modules/kallisto/0.43.1