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
 

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 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

+# 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/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 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
 

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 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

+# 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 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
 

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 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
 

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 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
 

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 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
 

src/.docker_modules/samtools/1.11/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/samtools:1.11
-docker build src/.docker_modules/samtools/1.11 -t 'lbmc/samtools:1.11'
-docker push lbmc/samtools:1.11
+# docker build src/.docker_modules/samtools/1.11 -t 'lbmc/samtools:1.11'
+# docker push lbmc/samtools:1.11
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samtools:1.11" --push src/.docker_modules/samtools/1.11

src/.docker_modules/samtools/1.14/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/samtools:1.14--hb421002_0 AS build
+
+# ldd /usr/local/bin/samtools
+#         linux-vdso.so.1 (0x00007ffec91ca000)
+#         libhts.so.3 => /usr/local/bin/../lib/libhts.so.3 (0x00007fa2fc31f000)
+#         libtinfow.so.6 => /usr/local/bin/../lib/libtinfow.so.6 (0x00007fa2fc2e0000)
+#         libncursesw.so.6 => /usr/local/bin/../lib/libncursesw.so.6 (0x00007fa2fc2a3000)
+#         libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa2fc11f000)
+#         libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x00007fa2fc105000)
+#         libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa2fc0e4000)
+#         libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa2fbf21000)
+#         libdeflate.so.0 => /usr/local/bin/../lib/./libdeflate.so.0 (0x00007fa2fbf11000)
+#         liblzma.so.5 => /usr/local/bin/../lib/./liblzma.so.5 (0x00007fa2fbee8000)
+#         libbz2.so.1.0 => /usr/local/bin/../lib/./libbz2.so.1.0 (0x00007fa2fbed4000)
+#         libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa2fbecf000)
+#         /lib64/ld-linux-x86-64.so.2 (0x00007fa2fc4af000)
+#         librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fa2fbec3000)
+
+ENV SAMTOOLS_VERSION=1.14
+ENV PACKAGES bash
+FROM alpine:3.8 AS env
+RUN apk update && \
+    apk add ${PACKAGES}
+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/samtools/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/samtools:1.14
+# docker build src/.docker_modules/samtools/1.14 -t 'lbmc/samtools:1.14'
+# docker push lbmc/samtools:1.14
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samtools:1.14" --push src/.docker_modules/samtools/1.14