src/.docker_modules/r-base/4.1.2/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/r-base:4.1.2
+# docker build src/.docker_modules/r-base/4.1.2 -t 'lbmc/r-base:4.1.2'
+# docker push lbmc/r-base:4.1.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r-base:4.1.2" --push src/.docker_modules/r-base/4.1.2

src/.docker_modules/rasusa/0.6.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/mbhall88/rasusa:0.6.0 AS quay_source
+
+FROM alpine:3.13
+COPY --from=quay_source /bin/rasusa /bin/
+RUN apk add --update --no-cache bash procps
+
+CMD [ "bash" ]

src/.docker_modules/rasusa/0.6.0/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/rasusa:0.6.0
+# docker build src/.docker_modules/rasusa/0.6.0 -t 'lbmc/rasusa:0.6.0'
+# docker push lbmc/rasusa:0.6.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/rasusa:0.6.0" --push src/.docker_modules/rasusa/0.6.0
+docker buildx build --platform linux/amd64,linux/arm64 -t 'lbmc/rasusa:0.6.0' --push src/.docker_modules/rasusa/0.6.0

src/.docker_modules/ribotricer/1.3.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:20.04
+MAINTAINER Emmanuel Labaronne
+
+ENV RIBOTRICER_VERSION=1.3.2
+ENV PACKAGES python3\
+             python3-dev\
+             python3-pip
+
+RUN apt-get update && \
+    apt-get install -y ${PACKAGES} && \
+    apt-get clean
+
+RUN pip3 install ribotricer==${RIBOTRICER_VERSION}

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

src/docker_modules/RSEM/1.3.0/Dockerfile → src/.docker_modules/rsem/1.3.0/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 RSEM_VERSION=1.3.0
 ENV BOWTIE2_VERSION=2.3.4.1
 ENV SAMTOOLS_VERSION=1.7
-ENV PACKAGES git=1:2.17.0* \
+ENV PACKAGES git=1:2.17* \
    build-essential=12.4* \
    ca-certificates=20180409 \
    zlib1g-dev=1:1.2.11* \

src/.docker_modules/rsem/1.3.0/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/rsem:1.3.0
+# docker build src/.docker_modules/rsem/1.3.0 -t 'lbmc/rsem:1.3.0'
+# docker push lbmc/rsem:1.3.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/rsem:1.3.0" --push src/.docker_modules/rsem/1.3.0

src/.docker_modules/sabre/039a55e/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.12.0
+MAINTAINER Lauret Modolo
+
+ENV SABRE_VERSION=039a55e
+
+ENV SABRE_DEPS g++ bash make zlib-dev git
+
+RUN echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/main" > /etc/apk/repositories \
+&& echo "http://ftp.acc.umu.se/mirror/alpinelinux.org/v3.11/community" >> /etc/apk/repositories \
+&& sed -i -e 's/v[[:digit:]]\..*\//edge\//g' /etc/apk/repositories \
+&& apk add --update --no-cache ${SABRE_DEPS} \
+&& git clone https://github.com/najoshi/sabre.git \
+&& cd sabre \
+&& git checkout $SABRE_VERSION \
+&& make \
+&& mv sabre /usr/bin \
+&& chmod +x /usr/bin/sabre
+
+
+CMD ["bash"]

src/.docker_modules/sabre/039a55e/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/sabre:039a55e
+# docker build src/.docker_modules/sabre/039a55e -t 'lbmc/sabre:039a55e'
+# docker push lbmc/sabre:039a55e
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/sabre:039a55e" --push src/.docker_modules/sabre/039a55e

src/docker_modules/Salmon/0.8.2/Dockerfile → src/.docker_modules/salmon/0.8.2/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/salmon/0.8.2/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/salmon:0.8.2
+# docker build src/.docker_modules/salmon/0.8.2 -t 'lbmc/salmon:0.8.2'
+# docker push lbmc/salmon:0.8.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/salmon:0.8.2" --push src/.docker_modules/salmon/0.8.2

src/.docker_modules/salmon/1.8.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+# image: COMBINE-lab/salmon
+# This dockerfile is based on the one created by
+# Titus Brown (available at https://github.com/ctb/2015-docker-building/blob/master/salmon/Dockerfile)
+FROM ubuntu:18.04
+MAINTAINER salmon.maintainer@gmail.com
+
+ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \
+    ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget
+ENV SALMON_VERSION 1.8.0
+
+# salmon binary will be installed in /home/salmon/bin/salmon
+
+### don't modify things below here for version updates etc.
+
+WORKDIR /home
+
+RUN apt-get update && \
+    apt remove -y libcurl4 && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | apt-key add -
+
+RUN apt-add-repository 'deb https://apt.kitware.com/ubuntu/ bionic main'
+
+RUN apt-get update
+
+RUN apt-key --keyring /etc/apt/trusted.gpg del C1F34CDD40CD72DA
+
+RUN apt-get install kitware-archive-keyring
+
+RUN apt-get install -y cmake
+
+RUN curl -k -L https://github.com/COMBINE-lab/salmon/archive/v${SALMON_VERSION}.tar.gz -o salmon-v${SALMON_VERSION}.tar.gz && \
+    tar xzf salmon-v${SALMON_VERSION}.tar.gz && \
+    cd salmon-${SALMON_VERSION} && \
+    mkdir build && \
+    cd build && \
+    cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local && make && make install
+
+# For dev version
+#RUN git clone https://github.com/COMBINE-lab/salmon.git && \
+#    cd salmon && \
+#    git checkout develop && \
+#    mkdir build && \
+#    cd build && \
+#    cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local && make && make install
+
+ENV PATH /home/salmon-${SALMON_VERSION}/bin:${PATH}
+ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}"
+
+RUN echo "export PATH=$PATH" > /etc/environment
+RUN echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH" > /etc/environment
\ No newline at end of file

src/.docker_modules/salmon/1.8.0/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/salmon:1.8.0
+docker build src/.docker_modules/salmon/1.8.0 -t 'lbmc/salmon:1.8.0'
+docker push lbmc/salmon:1.8.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/salmon:1.8.0" --push src/.docker_modules/salmon/1.8.0
\ No newline at end of file

src/.docker_modules/sambamba/0.6.7/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 SAMBAMBA_VERSION=0.6.7
+ENV PACKAGES curl=7.58.0* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*

src/.docker_modules/sambamba/0.6.7/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/sambamba:0.6.7
+# docker build src/.docker_modules/sambamba/0.6.7 -t 'lbmc/sambamba:0.6.7'
+# docker push lbmc/sambamba:0.6.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/sambamba:0.6.7" --push src/.docker_modules/sambamba/0.6.7

src/.docker_modules/sambamba/0.6.9/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 SAMBAMBA_VERSION=0.6.9
+ENV PACKAGES curl=7.58.0* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba-${SAMBAMBA_VERSION}-linux-static.gz -o sambamba_v${SAMBAMBA_VERSION}_linux.gz && \
+gunzip sambamba_v${SAMBAMBA_VERSION}_linux.gz && \
+mv sambamba_v${SAMBAMBA_VERSION}_linux /usr/bin/sambamba

src/.docker_modules/sambamba/0.6.9/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/sambamba:0.6.9
+# docker build src/.docker_modules/sambamba/0.6.9 -t 'lbmc/sambamba:0.6.9'
+# docker push lbmc/sambamba:0.6.9
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/sambamba:0.6.9" --push src/.docker_modules/sambamba/0.6.9

src/.docker_modules/samblaster/0.1.24/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 SAMBLASTER_VERSION=0.1.24
+ENV SAMTOOLS_VERSION=1.7
+ENV PACKAGES curl=7.58.0* \
+    samtools=${SAMTOOLS_VERSION}* \
+    ca-certificates=20180409 \
+    build-essential=12.4* \
+    zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean
+
+RUN curl -k -L https://github.com/GregoryFaust/samblaster/releases/download/v.${SAMBLASTER_VERSION}/samblaster-v.${SAMBLASTER_VERSION}.tar.gz -o samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+tar xvf samblaster-v.${SAMBLASTER_VERSION}.tar.gz && \
+cd samblaster-v.${SAMBLASTER_VERSION}/ && \
+make && \
+cp samblaster /usr/bin && \
+cd .. && \
+rm -R samblaster-v.${SAMBLASTER_VERSION}/

src/.docker_modules/samblaster/0.1.24/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/samblaster:0.1.24
+# docker build src/.docker_modules/samblaster/0.1.24 -t 'lbmc/samblaster:0.1.24'
+# docker push lbmc/samblaster:0.1.24
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samblaster:0.1.24" --push src/.docker_modules/samblaster/0.1.24

src/.docker_modules/samtools/1.11/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 SAMTOOLS_VERSION=1.11
+ENV PACKAGES git \
+             make \
+             gcc \
+             musl-dev \
+             zlib-dev \
+             ncurses-dev \
+             bzip2-dev \
+             xz-dev \
+             curl-dev \
+             bash
+
+RUN apk update && \
+    apk add ${PACKAGES}
+
+RUN git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION}  && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/