src/docker_modules/picard/2.18.11/Dockerfile → src/.docker_modules/picard/2.18.11/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/picard/2.18.11/PicardCommandLine → src/.docker_modules/picard/2.18.11/PicardCommandLine

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 set -eu
 PRG="$(basename -- "$0")"
 case "$PRG" in
@@ -12,4 +17,4 @@ PicardCommandLine)
         ;;
 esac
 
-exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"
+exec java -Xmx40g ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@"

src/.docker_modules/picard/2.18.11/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/picard:2.18.11
+# docker build src/.docker_modules/picard/2.18.11 -t 'lbmc/picard:2.18.11'
+# docker push lbmc/picard:2.18.11
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/picard:2.18.11" --push src/.docker_modules/picard/2.18.11

src/docker_modules/pigz/2.4/Dockerfile → src/.docker_modules/pigz/2.4/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/pigz/2.4/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/pigz:2.4
+# docker build src/.docker_modules/pigz/2.4 -t 'lbmc/pigz:2.4'
+# docker push lbmc/pigz:2.4
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/pigz:2.4" --push src/.docker_modules/pigz/2.4

src/.docker_modules/porechop/0.2.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+###############################################
+# Dockerfile to build poretools container image
+# Based on Ubuntu 16.04
+# Build with:
+#   sudo docker build -t poretools .
+###############################################
+
+# Use ubuntu 16.04 base image
+FROM ubuntu:16.04
+
+# File author/maintainer info
+MAINTAINER Sophie Lemoine <slemoine@biologie.ens.fr> and Charlotte Berthelier <bertheli@biologie.ens.fr>
+
+# Set non-interactive mode
+ENV DEBIAN_FRONTEND noninteractive
+
+ARG PACKAGE_VERSION=0.2.4
+ARG BUILD_PACKAGES="git python3 python3-pkg-resources build-essential"
+
+# Install dependencies
+RUN apt update && \
+    apt install --yes $BUILD_PACKAGES
+
+WORKDIR /tmp 
+RUN git clone https://github.com/rrwick/Porechop.git
+WORKDIR /tmp/Porechop 
+RUN git checkout v$PACKAGE_VERSION
+RUN python3 setup.py install && \
+    rm -rf /tmp/Porechop && \
+    apt remove --purge --yes git build-essential && \
+    apt autoremove --purge --yes
+
+# Set entrypoint so container can be used as executable
+ENTRYPOINT ["porechop"]
+CMD ["-h"]
\ No newline at end of file

src/.docker_modules/porechop/0.2.4/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/porechop:0.2.4
+docker build src/.docker_modules/porechop/0.2.4 -t 'lbmc/porechop:0.2.4'
+docker push lbmc/porechop:0.2.4
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/porechop:0.2.4" --push src/.docker_modules/porechop/0.2.4
\ No newline at end of file

src/.docker_modules/python/3.8/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM python:3.8.0a3-stretch
+MAINTAINER Remi Seraphin

src/.docker_modules/python/3.8/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/python:3.8
+# docker build src/.docker_modules/python/3.8 -t 'lbmc/python:3.8'
+# docker push lbmc/python:3.8
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/python:3.8" --push src/.docker_modules/python/3.8

src/.docker_modules/r-base/3.5.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM rocker/r-ver:3.5.3
+MAINTAINER Remi Seraphin
+
+RUN apt update && \
+apt install libssl-dev libcurl4-openssl-dev libxml2-dev zlib1g-dev git procps
+RUN R -e "install.packages('tidyverse'); \
+          install.packages('ggplot2')"

src/.docker_modules/r-base/3.5.3/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/r:3.5.3
+# docker build src/.docker_modules/r-base/3.5.3 -t 'lbmc/r:3.5.3'
+# docker push lbmc/r:3.5.3
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r:3.5.3" --push src/.docker_modules/r/3.5.3

src/.docker_modules/r-base/3.6.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.11.5
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~3.6.2 \
+  R-mathlib=~3.6.2 \
+  R-dev=~3.6.2
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  gcc \
+  gfortran \
+  icu-dev \
+  libjpeg-turbo \
+  libpng-dev \
+  openblas-dev \
+  pcre-dev \
+  readline-dev \
+  xz-dev \
+  zlib-dev \
+  bzip2-dev \
+  curl-dev \
+  libexecinfo-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 && \
+  apk add --update --no-cache ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]

src/.docker_modules/r-base/3.6.2/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:3.6.2
+# docker build src/.docker_modules/r-base/3.6.2 -t 'lbmc/r-base:3.6.2'
+# docker push lbmc/r-base:3.6.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r-base:3.6.2" --push src/.docker_modules/r-base/3.6.2

src/.docker_modules/r-base/4.0.0/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 R_PKGS R=~4.0.0 \
+  R-mathlib=~4.0.0 \
+  R-dev=~4.0.0
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  gcc \
+  gfortran \
+  icu-dev \
+  libjpeg-turbo \
+  libpng-dev \
+  openblas-dev \
+  pcre-dev \
+  readline-dev \
+  xz-dev \
+  zlib-dev \
+  bzip2-dev \
+  curl-dev \
+  libexecinfo-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 ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]

src/.docker_modules/r-base/4.0.0/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/r-base:4.0.0
+# docker build src/.docker_modules/r-base/4.0.0 -t 'lbmc/r-base:4.0.0'
+# docker push lbmc/r-base:4.0.0
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r-base:4.0.0" --push src/.docker_modules/r-base/4.0.0

src/.docker_modules/r-base/4.0.2/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 R_PKGS R=~4.0.2 \
+  R-mathlib=~4.0.2 \
+  R-dev=~4.0.2 \
+  R-doc=~4.0.2
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  icu-dev \
+  libjpeg-turbo \
+  pcre-dev \
+  readline-dev \
+  libexecinfo-dev \
+  file \
+  ttf-linux-libertine \
+  git \
+  openssl \
+  bash
+
+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 ${R_PKGS} ${R_DEPS}
+
+CMD ["R", "--no-save"]

src/.docker_modules/r-base/4.0.2/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/r-base:4.0.2
+# docker build src/.docker_modules/r-base/4.0.2 -t 'lbmc/r-base:4.0.2'
+# docker push lbmc/r-base:4.0.2
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r-base:4.0.2" --push src/.docker_modules/r-base/4.0.2

src/.docker_modules/r-base/4.0.3/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.13.1
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~4.0.3 \
+  R-mathlib=~4.0.3 \
+  R-dev=~4.0.3 \
+  R-doc=~4.0.3
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  icu-dev \
+  libjpeg-turbo \
+  pcre-dev \
+  readline-dev \
+  libexecinfo-dev \
+  file \
+  ttf-linux-libertine \
+  git \
+  openssl \
+  autoconf \
+  automake \
+  libuv \
+  http-parser \
+  tzdata \
+  libgit2-dev \
+  bash
+
+RUN apk add --update --no-cache ${R_PKGS} ${R_DEPS}

src/.docker_modules/r-base/4.0.3/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/r-base:4.0.3
+# docker build src/.docker_modules/r-base/4.0.3 -t 'lbmc/r-base:4.0.3'
+# docker push lbmc/r-base:4.0.3
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/r-base:4.0.3" --push src/.docker_modules/r-base/4.0.3

src/.docker_modules/r-base/4.1.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM alpine:3.15
+MAINTAINER Lauret Modolo
+
+ENV R_PKGS R=~4.1.2 \
+  R-mathlib=~4.1.2 \
+  R-dev=~4.1.2 \
+  R-doc=~4.1.2
+
+ENV R_DEPS g++ \
+  libxml2-dev \
+  make \
+  cmake \
+  linux-headers \
+  cairo-dev \
+  libxmu-dev \
+  pango-dev \
+  perl \
+  tiff-dev \
+  icu-dev \
+  libjpeg-turbo \
+  pcre-dev \
+  readline-dev \
+  libexecinfo-dev \
+  file \
+  ttf-linux-libertine \
+  git \
+  openssl \
+  autoconf \
+  automake \
+  libuv \
+  http-parser \
+  tzdata \
+  libgit2-dev \
+  bash
+
+RUN apk add --update --no-cache ${R_PKGS} ${R_DEPS}