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# 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 FASTQC_VERSION=0.11.5
ENV PACKAGES fastqc=${FASTQC_VERSION}*
ENV PACKAGES fastqc=${FASTQC_VERSION}* \
perl=5.26*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
......
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/fastqc:0.11.5
# docker build src/.docker_modules/fastqc/0.11.5 -t 'lbmc/fastqc:0.11.5'
# docker push lbmc/fastqc:0.11.5
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastqc:0.11.5" --push src/.docker_modules/fastqc/0.11.5
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM ubuntu:18.04
MAINTAINER Laurent Modolo
......
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/file_handle:0.1.1
# docker build src/.docker_modules/file_handle/0.1.1 -t 'lbmc/file_handle:0.1.1'
# docker push lbmc/file_handle:0.1.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/file_handle:0.1.1" --push src/.docker_modules/file_handle/0.1.1
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM python:3.9-slim
MAINTAINER Lauret Modolo
ENV FLEXI_SPLITTER_VERSION=1.0.2
RUN apt-get update -qq \
&& apt-get install --no-install-recommends --yes \
build-essential \
procps
RUN pip3 install flexi-splitter==${FLEXI_SPLITTER_VERSION}
RUN apt-get remove --yes \
build-essential
CMD [ "bash" ]
\ No newline at end of file
#!/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
# 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
#!/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
# 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
#!/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
# 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"]
#!/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
# 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
#!/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
# 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/
#!/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
# 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/
#!/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
# 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/
#!/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