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 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

src/.docker_modules/samtools/1.7/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=1.7
+ENV PACKAGES git \
+             make \
+             gcc \
+             musl-dev \
+             zlib-dev \
+             ncurses-dev \
+             bzip2-dev \
+             xz-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/

src/.docker_modules/samtools/1.7/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/samtools:1.7
+# docker build src/.docker_modules/samtools/1.7 -t 'lbmc/samtools:1.7'
+# docker push lbmc/samtools:1.7
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samtools:1.7" --push src/.docker_modules/samtools/1.7

src/.docker_modules/sanity/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+##### BASE IMAGE #####
+FROM ubuntu:18.04
+
+##### METADATA #####
+LABEL base.image="ubuntu:18.04"
+LABEL version="1"
+LABEL software="Sanity"
+LABEL software.version="1.0"
+LABEL software.description="Sanity"
+LABEL software.website=""
+LABEL software.documentation="https://github.com/jmbreda/Sanity"
+
+##### VARIABLES #####
+
+# Use variables for convenient updates/re-usability
+ENV SOFTWARE_VERSION 1.0
+
+RUN apt-get update \
+  && apt-get install -y tzdata \
+  && ln -fs /usr/share/zoneinfo/Europe/Berlin /etc/localtime \
+  && dpkg-reconfigure --frontend noninteractive tzdata \
+  && apt-get install --yes git make g++ libgomp1 \
+  && git clone https://github.com/jmbreda/Sanity.git \
+  && cd Sanity \
+  && cd src \
+  && make \
+  && cp ../bin/Sanity /usr/bin \
+  && cd ../../ \
+  && rm -rf Sanity \
+  && apt-get remove --purge --yes git make g++ \

src/.docker_modules/sanity/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 mlepetit/sanity
+docker build src/.docker_modules/sanity -t 'lbmc/sanity'
+docker push lbmc/sanity

src/.docker_modules/seqkit/2.1.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:16.04
+
+#Begin: install prerequisites
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        build-essential \
+        curl \
+        git \
+        libcurl3-dev \
+        libfreetype6-dev \
+        libpng12-dev \
+        libzmq3-dev \
+        locate \
+        pkg-config \
+        rsync \
+        software-properties-common \
+        sudo \
+        unzip \
+        wget \
+        zip \
+        zlib1g-dev \
+        && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+#End: install prerequisites
+
+#Begin: install golang
+ENV GOLANG_DOWNLOAD_URL https://golang.org/dl/go1.17.9.linux-amd64.tar.gz
+ENV GOPATH $HOME/go
+ENV PATH $PATH:/usr/local/go/bin:$GOPATH/bin
+RUN curl -fsSL "$GOLANG_DOWNLOAD_URL" -o golang.tar.gz && \
+    sudo tar -C /usr/local -xzf golang.tar.gz && \
+    rm golang.tar.gz && \
+    mkdir -p "$GOPATH/src" "$GOPATH/bin" && chmod -R 777 "$GOPATH"
+#End: install golang
+
+#Begin: install delve
+RUN go install github.com/go-delve/delve/cmd/dlv@latest 
+#1.8.3
+#End: install delve
+
+#Begin: install seqkit
+RUN go install github.com/shenwei356/seqkit/v2/seqkit@v2.1.0
+
+#2.1.0
+#End: install seqkit
+
+WORKDIR $HOME/go/src/github.com/shenwei356/seqkit
\ No newline at end of file

src/.docker_modules/seqkit/2.1.0/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/seqkit:2.1.0
+docker build src/.docker_modules/seqkit/2.1.0 -t 'lbmc/seqkit:2.1.0'
+docker push lbmc/seqkit:2.1.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/seqkit:2.1.0" --push src/.docker_modules/seqkit/2.1.0
\ No newline at end of file

src/docker_modules/SRAtoolkit/2.8.2/Dockerfile → src/.docker_modules/sratoolkit/2.8.2/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/sratoolkit/2.8.2/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/sratoolkit:2.8.2
+# docker build src/.docker_modules/sratoolkit/2.8.2 -t 'lbmc/sratoolkit:2.8.2'
+# docker push lbmc/sratoolkit:2.8.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/sratoolkit:2.8.2" --push src/.docker_modules/sratoolkit/2.8.2

src/.docker_modules/sratoolkit/3.0.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ncbi/sra-tools:3.0.0
+
+ENV SRATOOLKIT_VERSION=3.0.0
+ENV PACKAGES bash 
+
+RUN apk add ${PACKAGES}

src/.docker_modules/sratoolkit/3.0.0/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/sratoolkit:3.0.0
+# docker build src/.docker_modules/sratoolkit/3.0.0 -t 'lbmc/sratoolkit:3.0.0'
+# docker push lbmc/sratoolkit:3.0.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/sratoolkit:3.0.0" --push src/.docker_modules/sratoolkit/3.0.0

src/.docker_modules/star/2.5.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/star:2.7.3a--0
+MAINTAINER Laurent Modolo

src/.docker_modules/star/2.5.3/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/star:2.7.3a
+# docker build src/.docker_modules/star/2.7.3a/ -t 'lbmc/star:2.7.3a'
+# docker push lbmc/star:2.7.3a
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/star:2.7.3a" --push src/.docker_modules/star/2.7.3a

src/.docker_modules/star/2.7.3a/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/star:2.7.3a--0
+MAINTAINER Laurent Modolo

src/.docker_modules/star/2.7.3a/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/star:2.7.3a
+# docker build src/.docker_modules/star/2.7.3a/ -t 'lbmc/star:2.7.3a'
+# docker push lbmc/star:2.7.3a
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/star:2.7.3a" --push src/.docker_modules/star/2.7.3a

src/.docker_modules/stringtie/2.1.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM ubuntu:16.04
+Maintainer Chen Yuelong <yuelong.chen.btr@gmail.com>
+
+ARG version=2.1.1
+RUN mkdir -p /opt/tools
+
+WORKDIR /opt/tools
+
+# install stringtie
+RUN \
+  apt update && apt install -y wget && \
+  wget -c http://ccb.jhu.edu/software/stringtie/dl/stringtie-${version}.Linux_x86_64.tar.gz && \
+  tar -zxvf stringtie-${version}.Linux_x86_64.tar.gz && \
+  cp stringtie-${version}.Linux_x86_64/stringtie /usr/local/bin && \
+  rm -rf stringtie* && \
+  apt-get remove --purge --yes \
+              wget && \
+  apt-get autoremove --purge --yes && \
+  apt-get clean

src/.docker_modules/stringtie/2.1.1/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/stringtie:2.1.1
+docker build src/.docker_modules/stringtie/2.1.1 -t 'lbmc/stringtie:2.1.1'
+docker push lbmc/stringtie:2.1.1
+# docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/stringtie:2.1.1" --push src/.docker_modules/stringtie/2.1.1

src/.docker_modules/subread/1.6.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM quay.io/biocontainers/subread:1.6.4--h84994c4_1
+MAINTAINER Laurent Modolo