src/docker_modules/file_handle/0.1.1/Dockerfile → src/.docker_modules/file_handle/0.1.1/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/file_handle/0.1.1/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/file_handle:0.1.1
+# docker build src/.docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
+# docker push lbmc/file_handle:0.1.1
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/file_handle:0.1.1" --push src/.docker_modules/file_handle/0.1.1

src/.docker_modules/flexi_splitter/1.0.2/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 FLEXI_SPLITTER_VERSION=1.0.2
+RUN apt-get update -qq \
+    && apt-get install --no-install-recommends --yes \
+        build-essential \
+        procps
+RUN pip3 install flexi-splitter==${FLEXI_SPLITTER_VERSION}
+RUN apt-get remove --yes \
+        build-essential
+
+CMD [ "bash" ]
\ No newline at end of file

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 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 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 \
+    && /opt/conda/bin/conda config --add channels bioconda \
+    && /opt/conda/bin/conda install --yes \
+        -c kbchoi g2gtools pycparser setuptools\
+        nomkl \
+    && /opt/conda/bin/conda clean -afy \
+    && find /opt/conda/ -follow -type f -name '*.a' -delete \
+    && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
+    && find /opt/conda/ -follow -type f -name '*.js.map' -delete
+

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 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
+
+ENV G2GTOOLS_VERSION=0.2.8
+
+RUN apt update \
+ && apt install -y wget build-essential zlib1g-dev libbz2-dev liblzma-dev procps \
+ && wget https://github.com/churchill-lab/g2gtools/archive/v${G2GTOOLS_VERSION}.tar.gz \
+ && tar -xvf v${G2GTOOLS_VERSION}.tar.gz \
+ && cd g2gtools-${G2GTOOLS_VERSION} \
+ && pip install numpy \
+ && pip install pysam \
+ && make install 
+
+
+CMD ["bash"]

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 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
+
+ENV GATK_VERSION=3.8.0
+
+RUN echo "#\!/bin/sh\njava -jar /usr/GenomeAnalysisTK.jar \$@" > /bin/gatk3 
+RUN chmod +x /bin/gatk3
+RUN sed -i 's/java/java -Xmx128g/g' /bin/gatk3

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 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
+
+ENV GATK_VERSION=4.0.8.1
+
+RUN cp gatk /usr/bin/

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 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
+
+ENV GFFREAD_VERSION=0.11.8
+ENV PACKAGES make \
+             g++ \
+             bash \
+             perl
+
+RUN apk update && \
+    apk add ${PACKAGES} && \
+wget http://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_VERSION}.tar.gz && \
+tar -xvf gffread-${GFFREAD_VERSION}.tar.gz && \
+cd gffread-${GFFREAD_VERSION}/ && \
+make && \
+cp gffread /usr/bin/

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 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
+
+ENV GFFREAD_VERSION=0.12.2
+ENV PACKAGES make \
+             g++ \
+             bash \
+             perl
+
+RUN apk update && \
+    apk add ${PACKAGES} && \
+wget http://ccb.jhu.edu/software/stringtie/dl/gffread-${GFFREAD_VERSION}.tar.gz && \
+tar -xvf gffread-${GFFREAD_VERSION}.tar.gz && \
+cd gffread-${GFFREAD_VERSION}/ && \
+make && \
+cp gffread /usr/bin/

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 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
+