src/.docker_modules/bedtools/2.30.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1
\ No newline at end of file

src/.docker_modules/bedtools/2.30.0/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/bedtools:2.30.0
+docker build src/.docker_modules/bedtools/2.30.0 -t 'lbmc/bedtools:2.30.0'
+docker push lbmc/bedtools:2.30.0

src/docker_modules/MACS2/2.1.0/Dockerfile → src/.docker_modules/bioawk/1.0/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 MACS_VERSION=2.1.1.20160309
+ENV BIOAWK_VERSION=1.0
 ENV PACKAGES git=1:2.17* \
    build-essential=12.4* \
-   python-pip=9.0.1* \
    ca-certificates=20180409 \
-   python-setuptools=39.0.1* \
-   python-dev=2.7* \
-   python-numpy=1:1.13* \
-   python-wheel=0.30.0* \
-   zlib1g-dev=1:1.2.11*
+   zlib1g-dev=1:1.2.11* \
+   byacc
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends ${PACKAGES} && \
     apt-get clean
 
-RUN pip install MACS2==${MACS_VERSION}
-
+RUN git clone https://github.com/lh3/bioawk.git && \
+  cd bioawk && \
+  git checkout tags/v${BIOAWK_VERSION} && \
+  make && \
+  cd .. && \
+  mv bioawk/bioawk /usr/bin/ && \
+  rm -Rf bioawk

src/.docker_modules/bioawk/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/bioawk:1.0
+# docker build src/.docker_modules/bioawk/1.0 -t 'lbmc/bioawk:1.0'
+# docker push lbmc/bioawk:1.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bioawk:1.0" --push src/.docker_modules/bioawk/1.0

src/.docker_modules/bioconvert/0.4.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM bioconvert/bioconvert:test
+MAINTAINER Laurent Modolo
+
+ENV BIOCONVERT_VERSION="0.4.0"
\ No newline at end of file

src/.docker_modules/bioconvert/0.4.0/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/bioconvert:0.4.0
+# docker build src/.docker_modules/bioconvert/0.4.0 -t 'lbmc/bioconvert:0.4.0'
+# docker push lbmc/bioconvert:0.4.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bioconvert:0.4.0" --push src/.docker_modules/bioconvert/0.4.0

src/.docker_modules/bioconvert/0.4.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM conda/miniconda3
+MAINTAINER Laurent Modolo
+
+ENV BIOCONVERT_VERSION="0.4.3"
+RUN 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 bioconvert
+SHELL ["conda", "run", "-n", "bioconvert", "/bin/bash", "-c"]
+RUN conda install bioconvert \
+&& echo "conda activate bioconvert" >> /root/.bashrc
+RUN apt update && apt install -y procps
+
+ENV PATH /usr/local/envs/bioconvert/bin:/usr/local/condabin:$PATH

src/.docker_modules/bioconvert/0.4.3/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/bioconvert:0.4.3
+# docker build src/.docker_modules/bioconvert/0.4.3 -t 'lbmc/bioconvert:0.4.3'
+# docker push lbmc/bioconvert:0.4.3
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bioconvert:0.4.3" --push src/.docker_modules/bioconvert/0.4.3

src/docker_modules/Bowtie/1.2.2/Dockerfile → src/.docker_modules/bowtie/1.2.2/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
 

src/.docker_modules/bowtie/1.2.2/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/bowtie:1.2.2
+# docker build src/.docker_modules/bowtie/1.2.2 -t 'lbmc/bowtie:1.2.2'
+# docker push lbmc/bowtie:1.2.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bowtie:1.2.2" --push src/.docker_modules/bowtie/1.2.2

src/docker_modules/Bowtie2/2.3.4.1/Dockerfile → src/.docker_modules/bowtie2/2.3.4.1/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
 

src/.docker_modules/bowtie2/2.3.4.1/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/bowtie2:2.3.4.1
+# docker build src/.docker_modules/bowtie2/2.3.4.1 -t 'lbmc/bowtie2:2.3.4.1'
+# docker push lbmc/bowtie2:2.3.4.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bowtie2:2.3.4.1" --push src/.docker_modules/bowtie2/2.3.4.1

src/docker_modules/BWA/0.7.17/Dockerfile → src/.docker_modules/bwa/0.7.17/Dockerfile

-FROM ubuntu:18.04
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM lbmc/samtools:1.11
 MAINTAINER Laurent Modolo
 
 ENV BWA_VERSION=0.7.17
-ENV PACKAGES curl=7.58.0* \
-    ca-certificates=20180409 \
-    build-essential=12.4* \
-    zlib1g-dev=1:1.2.11*
+ENV SAMBLASTER_VERSION=0.1.24
+
+ENV PACKAGES curl \
+  g++
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    apt-get clean
+RUN apk update && \
+    apk add ${PACKAGES}
 
 RUN curl -k -L https://github.com/lh3/bwa/releases/download/v${BWA_VERSION}/bwa-${BWA_VERSION}.tar.bz2 -o bwa-v${BWA_VERSION}.tar.bz2 && \
 tar xjf bwa-v${BWA_VERSION}.tar.bz2 && \
@@ -18,3 +21,4 @@ make && \
 cp bwa /usr/bin && \
 cd .. && \
 rm -R bwa-${BWA_VERSION}/
+

src/.docker_modules/bwa/0.7.17/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/bwa:0.7.17
+# docker build src/.docker_modules/bwa/0.7.17 -t 'lbmc/bwa:0.7.17'
+# docker push lbmc/bwa:0.7.17
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bwa:0.7.17" --push src/.docker_modules/bwa/0.7.17

src/docker_modules/canu/1.6/Dockerfile → src/.docker_modules/canu/1.6/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
 

src/.docker_modules/canu/1.6/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/canu:1.6
+# docker build src/.docker_modules/canu/1.6 -t 'lbmc/canu:1.6'
+# docker push lbmc/canu:1.6
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/canu:1.6" --push src/.docker_modules/canu/1.6

src/.docker_modules/cellphonedb/3.0.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.7-slim 
+
+ENV RPY2_CFFI_MODE=ABI
+
+RUN mkdir /app /docker
+COPY requirements.txt /app
+COPY requirements-web.txt /app
+WORKDIR /app
+
+RUN pip install -r requirements.txt
+RUN pip install -r requirements-web.txt
+RUN pip install cellphonedb==3.0.0
+
+
+COPY . /app
+COPY ./docker /docker
+RUN mkdir -p /var/log/uwsgi
+RUN touch /var/log/uwsgi/cellphonedb.log
+RUN chmod +x /app
+
+CMD ["/docker/run-system.sh"]

src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini

+[uwsgi]
+module = wsgi:app
+
+master = true
+processes = 4
+
+
+socket = 0.0.0.0:5000
+chmod-socket = 660
+vacuum = true
+
+die-on-term = true
+
+stats = /tmp/stats.socket
\ No newline at end of file

src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini.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/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