src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM postgres:9.6
+
+ENV POSTGRES_PASSWORD  root
+ENV POSTGRES_USER root
+ENV POSTGRES_DB cellphonedb
\ No newline at end of file

src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh

+#!/bin/bash
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+exec uwsgi --ini cellphonedb.ini --log-master

src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt

+flask>=1.1,<1.1.99
+Flask-RESTful>=0.3,<0.3.99
+Flask-Testing>=0.8,<0.8.99
+pika>=0.12,<0.12.99
+boto3>=1.7,<1.7.99
+uWSGI>=2.0,<2.0.99

src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/.docker_modules/cellphonedb/3.0.0/requirements.txt

+click>=7.0,<8.0
+pandas>=1.0.0,<=1.1.4
+numpy>=1.16.5,<=1.19.5
+numpy-groupies
+scikit-learn==0.22
+flask>=1.0,<2.0.0
+Flask-RESTful>=0.3
+Flask-Testing>=0.7
+SQLAlchemy>=1.3,<1.4
+PyYAML>=5.4,<6.0
+requests>=2.25,<3.0
+pika>=1.0.0,<2.0
+boto3>=1.15,<2.0
+geosketch==0.3
+rpy2>=3.4.0,<4.0
+tqdm>=4.3,<5.0
+h5py<3.0.0
+anndata>=0.7,<=0.75

src/.docker_modules/cellphonedb/3.0.0/requirements.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/.docker_modules/clustalo/1.2.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch-slim
+
+ENV CLUSTALO_VERSION=1.2.4-1
+ENV PACKAGES clustalo=${CLUSTALO_VERSION} \
+  procps 
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/clustalo/1.2.4/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/clustalo:1.2.4
+# docker build src/.docker_modules/clustalo/1.2.4 -t 'lbmc/clustalo:1.2.4'
+# docker push lbmc/clustalo:1.2.4
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/clustalo:1.2.4" --push src/.docker_modules/clustalo/1.2.4

src/.docker_modules/crossmap/0.4.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/crossmap:0.4.1--pyh5ca1d4c_0
+MAINTAINER Laurent Modolo

src/.docker_modules/crossmap/0.4.1/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/crossmap:0.4.1
+# docker build src/.docker_modules/crossmap/0.4.1/ -t 'lbmc/crossmap:0.4.1'
+# docker push lbmc/crossmap:0.4.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/crossmap:0.4.1" --push src/.docker_modules/crossmap/0.4.1

src/.docker_modules/cutadapt/1.14/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 CUTADAPT_VERSION=1.14
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}

src/.docker_modules/cutadapt/1.14/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/cutadapt:1.14
+# docker build src/.docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
+# docker push lbmc/cutadapt:1.14
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cutadapt:1.14" --push src/.docker_modules/cutadapt/1.14

src/.docker_modules/cutadapt/1.15/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 CUTADAPT_VERSION=1.15
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}

src/.docker_modules/cutadapt/1.15/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/cutadapt:1.15
+# docker build src/.docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
+# docker push lbmc/cutadapt:1.15
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cutadapt:1.15" --push src/.docker_modules/cutadapt/1.15

src/.docker_modules/cutadapt/2.1/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 CUTADAPT_VERSION=2.1
+ENV PACKAGES bash \
+             python3 \
+             python3-dev \
+             musl-dev \
+             gcc
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN pip3 install --upgrade pip && \
+  pip3 install cutadapt==${CUTADAPT_VERSION}
+
+

src/.docker_modules/cutadapt/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/cutadapt:2.1
+# docker build src/.docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
+# docker push lbmc/cutadapt:2.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/cutadapt:2.1" --push src/.docker_modules/cutadapt/2.1

src/.docker_modules/danpos3/2f7f223/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:20.04 
+
+ENV DANPOS_VERSION="2f7f223"
+ENV TZ=Europe/Paris
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone \
+&& apt update -qq \
+&& apt install --no-install-recommends software-properties-common -y dirmngr git python \
+&& wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
+&& add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN apt-get update \
+&& apt-get install -y r-base=4.0.1 samtools \
+&& git clone https://github.com/sklasfeld/DANPOS3.git \
+&& cd DANPOS3 \
+&& git checkout $DANPOS_VERSION \
+&& pip install -r requirements.txt \
+&& chmod +x DANPOS3/*.py
+
+ENV PATH="/DANPOS3:${PATH}"
+CMD [ "bash" ]

src/.docker_modules/danpos3/2f7f223/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/danpos3:2f7f223
+# docker build src/.docker_modules/danpos3/2f7f223 -t 'lbmc/danpos3:2f7f223'
+# docker push lbmc/danpos3:2f7f223
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/danpos3:2f7f223" --push src/.docker_modules/danpos3/2f7f223

src/docker_modules/deepTools/3.0.2/Dockerfile → src/.docker_modules/deeptools/3.0.2/Dockerfile

-FROM ubuntu:18.04
+# 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=3.0.2
-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* \
-             zlib1g-dev=1:1.2.11* \
-             libcurl4-gnutls-dev=7.58.0*
+ENV PACKAGES build-essential \
+             python3-pip \
+             python3-setuptools \
+             python3-dev \
+             python3-wheel \
+             zlib1g-dev \
+             procps \
+             libcurl4-gnutls-dev
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \

src/.docker_modules/deeptools/3.0.2/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/deeptools:3.0.2
+# docker build src/.docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
+# docker push lbmc/deeptools:3.0.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.0.2" --push src/.docker_modules/deeptools/3.0.2