Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • cginevra/nextflow
  • LBMC/Palladino/RNAseq_nextflow
  • fmortreu/nextflow
  • rseraphi/nextflow
  • elabaron/nextflow
  • acorbin/nextflow
  • cfournea/nextflow
  • pberna01/nextflow
  • jblin/nextflow
  • LBMC/RMI2/rmi2_pipelines
  • carpin/nextflow
  • dtorresc/nextflow
  • nlecouvr/nextflow-nathan
  • ggirau03/nextflow
  • LBMC/nextflow
  • lpicard/nextflow
  • letien02/nextflow
  • ogandril/nextflow
  • mparis/nextflow
  • lanani/nextflow
  • mshamjal/nextflow
  • mcariou/nextflow
  • fduveau/nextflow
  • jshapiro/nextflow
  • yjia01/nextflow
  • pmarie01/nextflow
  • jclaud01/nextflow
  • mprieux/nextflow
  • hpolvech/nextflow
  • rhoury/nextflow
  • alapendr/nextflow
  • cbourgeo/nextflow
  • jvalat/nextflow
  • z483800/nextflow
  • hregue/nextflow
  • dchalopi/nextflow
  • mherbett/nextflow
  • jprobin/nextflow
  • lestrada/nextflow
  • z483801/nextflow
  • ecombe01/nextflow
  • lgely/nextflow
  • gyvert/nextflow
  • nfontrod/nextflow
  • gbenoit/nextflow
  • aguill09/nextflow
  • LBMC/regards/nextflow
  • mvilcot/nextflow
  • jkleine/nextflow
  • jseimand/nextflow
  • mdjaffar/nextflow
  • LBMC/Delattre/JU28_59vs17_SNP
  • mlepetit/nextflow
  • vvanoost/nextflow
54 results
Show changes
Showing
with 248 additions and 1 deletion
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM debian:stretch
MAINTAINER Laurent Modolo
ENV DEEPTOOLS_VERSION=3.1.1
ENV PACKAGES build-essential \
python3-pip \
python3-setuptools \
python3-dev \
python3-wheel \
zlib1g-dev \
libcurl4-gnutls-dev \
procps
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN pip3 install deeptools==${DEEPTOOLS_VERSION}
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/deeptools:3.1.1
# docker build src/.docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
# docker push lbmc/deeptools:3.1.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.1.1" --push src/.docker_modules/deeptools/3.1.1
# 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 DEEPTOOLS_VERSION=3.5.0
RUN apt-get update -qq \
&& apt-get install --no-install-recommends --yes \
build-essential \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
libssl-dev \
libncurses5-dev \
procps
RUN pip3 install deeptools==${DEEPTOOLS_VERSION}
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/deeptools:3.5.0
# docker build src/.docker_modules/deeptools/3.5.0 -t 'lbmc/deeptools:3.5.0'
# docker push lbmc/deeptools:3.5.0
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.5.0" --push src/.docker_modules/deeptools/3.5.0
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM python:3.8-slim
MAINTAINER Lauret Modolo
ENV DEEPTOOLS_VERSION=3.5.1
RUN apt-get update -qq \
&& apt-get install --no-install-recommends --yes \
build-essential \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
libssl-dev \
libncurses5-dev \
libcurl4 \
libc6 \
procps
RUN pip3 install pysam deeptools==${DEEPTOOLS_VERSION}
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/deeptools:3.5.1
# docker build src/.docker_modules/deeptools/3.5.1 -t 'lbmc/deeptools:3.5.1'
# docker push lbmc/deeptools:3.5.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/deeptools:3.5.1" --push src/.docker_modules/deeptools/3.5.1
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
fd "Dockerfile" src/.docker_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker push lbmc/"$0)}'
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
fd "Dockerfile" src/.docke_modules | perl -pe 's|.*docker_modules/(.*)/(.*)/Dockerfile|\1:\2|g' | awk '{system("docker tag "$0" lbmc/" $0)}'
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM debian:buster as build
MAINTAINER Laurent Modolo
ENV EMASEZERO_VERSION=0.3.1
ENV PACKAGES build-essential \
ca-certificates \
zlib1g-dev \
git
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
apt-get clean
RUN git clone https://github.com/churchill-lab/emase-zero.git \
&& cd emase-zero/src/ \
&& make \
&& mv emase-zero /usr/local/bin/ \
&& ldd /usr/local/bin/emase-zero
# linux-vdso.so.1 (0x00007ffe8e35f000)
# libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fbd358b5000)
# libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fbd35731000)
# libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fbd355ae000)
# libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fbd35594000)
# libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fbd353d3000)
# /lib64/ld-linux-x86-64.so.2 (0x00007fbd35af7000)
FROM debian:buster-slim
COPY --from=build /usr/local/bin/emase-zero /usr/local/bin/
COPY --from=build /lib/x86_64-linux-gnu/libz.so.1 /lib/x86_64-linux-gnu/
COPY --from=build /lib/x86_64-linux-gnu/libm.so.6 /lib/x86_64-linux-gnu/
COPY --from=build /lib/x86_64-linux-gnu/libgcc_s.so.1 /lib/x86_64-linux-gnu/
RUN apt-get update && \
apt-get install -y procps bash
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/emase-zero:0.3.1
# docker build src/.docker_modules/emase-zero/0.3.1 -t 'lbmc/emase-zero:0.3.1'
# docker push lbmc/emase-zero:0.3.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/emase-zero:0.3.1" --push src/.docker_modules/emase-zero/0.3.1
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM conda/miniconda2
MAINTAINER Laurent Modolo
ENV EMASE_VERSION=0.10.16
RUN conda init \
&& conda config --add channels r \
&& conda config --add channels bioconda \
&& conda create -y -n emase jupyter
SHELL ["conda", "run", "-n", "emase", "/bin/bash", "-c"]
RUN conda install -y -c kbchoi emase \
&& echo "conda activate emase" >> /root/.bashrc
RUN apt update && apt install -y procps
ENV PATH /usr/local/envs/emase/bin:/usr/local/condabin:$PATH
#!/bin/sh
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
docker pull lbmc/emase:0.10.16
# docker build src/.docker_modules/emase/0.10.16 -t 'lbmc/emase:0.10.16'
# docker push lbmc/emase:0.10.16
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/emase:0.10.16" --push src/.docker_modules/emase/0.10.16
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0
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/fastp:0.19.7
# docker build src/.docker_modules/fastp/0.19.7 -t 'lbmc/fastp:0.19.7'
# docker push lbmc/fastp:0.19.7
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.19.7" --push src/.docker_modules/fastp/0.19.7
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM quay.io/biocontainers/fastp:0.20.1--h8b12597_0
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/fastp:0.20.1
# docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1'
# docker push lbmc/fastp:0.20.1
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.20.1" --push src/.docker_modules/fastp/0.20.1
# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
#
# SPDX-License-Identifier: AGPL-3.0-or-later
FROM quay.io/biocontainers/fastp:0.23.2--hb7a2d85_2
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/fastp:0.23.2
# docker build src/.docker_modules/fastp/0.23.2 -t 'lbmc/fastp:0.23.2'
docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/fastp:0.23.2" --push src/.docker_modules/fastp/0.23.2
docker push lbmc/fastp:0.23.2
# 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