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[WIP][ENH] add Dockerfile for python version og GLM single #46

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5dfcecd
pin minimum python and dependencies versions
Remi-Gau Apr 7, 2022
0b5004a
add Dockerfile
Remi-Gau Apr 11, 2022
0e6062b
add singularity recipe
Remi-Gau Apr 28, 2022
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127 changes: 127 additions & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -0,0 +1,127 @@
# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.8.0
# Timestamp: 2022/04/11 12:55:39 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/ReproNim/neurodocker
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@Remi-Gau Remi-Gau Apr 11, 2022

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This file is automatically generated via the Makefile


FROM python:3.9.12-slim-buster

USER root

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
&& chmod 777 /opt && chmod a+s /opt \
&& mkdir -p /neurodocker \
&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
build-essential \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

COPY ["glmsingle", "setup.py", "MANIFEST.in", "README.md", "requirements.txt", "/glmsingle/"]

WORKDIR /glmsingle

RUN pip install .

RUN pip install jupyterlab

EXPOSE 8888

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

WORKDIR /home/neuro

COPY ["examples", "/home/neuro/examples"]

RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "python:3.9.12-slim-buster" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "build-essential" \
\n ] \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n "glmsingle", \
\n "setup.py", \
\n "MANIFEST.in", \
\n "README.md", \
\n "requirements.txt", \
\n "/glmsingle/" \
\n ] \
\n ], \
\n [ \
\n "workdir", \
\n "/glmsingle" \
\n ], \
\n [ \
\n "run", \
\n "pip install ." \
\n ], \
\n [ \
\n "run", \
\n "pip install jupyterlab" \
\n ], \
\n [ \
\n "expose", \
\n [ \
\n "8888" \
\n ] \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuro" \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n "examples", \
\n "/home/neuro/examples" \
\n ] \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
46 changes: 45 additions & 1 deletion Makefile
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Expand Up @@ -113,4 +113,48 @@ coverage-python: ## check code coverage quickly with the default Python
install: clean ## install the package to the active Python's site-packages
python setup.py install

################################################################################
################################################################################

################################################################################
# DOCKER

.PHONY: Dockerfile glmsingle.def
Dockerfile:
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base python:3.9.12-slim-buster \
--pkg-manager apt \
--install "build-essential" \
--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /glmsingle/ \
--workdir /glmsingle \
--run "pip install ." \
--run "pip install jupyterlab" \
--expose 8888 \
--user neuro \
--workdir /home/neuro \
--copy examples /home/neuro/examples > Dockerfile
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@Remi-Gau Remi-Gau Apr 11, 2022

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This is the neurodocker command to build the Dockerfile for GLMsingle


docker_build: Dockerfile
docker build . -t glmsingle:latest

docker_run: docker_build
mkdir -p $$PWD/tmp
docker run -it --rm \
--publish 8888:8888 \
--volume $$PWD/tmp:/home/neuro/tmp \
glmsingle:latest \
jupyter-lab --no-browser --ip 0.0.0.0

glmsingle.def:
docker run --rm repronim/neurodocker:0.7.0 generate singularity \
--base python:3.9.12-slim-buster \
--pkg-manager apt \
--install "build-essential" \
--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /home/glmsingle/ \
--workdir /glmsingle \
--run "pip install ." \
--user neuro \
--workdir /home/neuro \
--copy examples /home/neuro/examples > glmsingle.def

singularity_build: glmsingle.def
sudo singularity build glmsingle.sif glmsingle.def
113 changes: 113 additions & 0 deletions Singularity
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# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.8.0
# Timestamp: 2022/04/28 15:50:25 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/ReproNim/neurodocker

FROM python:3.9.12-slim-buster

USER root

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* \
&& sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
&& dpkg-reconfigure --frontend=noninteractive locales \
&& update-locale LANG="en_US.UTF-8" \
&& chmod 777 /opt && chmod a+s /opt \
&& mkdir -p /neurodocker \
&& if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi \
&& chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
build-essential \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

COPY ["glmsingle", "setup.py", "MANIFEST.in", "README.md", "requirements.txt", "/glmsingle/"]

WORKDIR /glmsingle

RUN pip install .

RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
USER neuro

WORKDIR /home/neuro

COPY ["examples", "/home/neuro/examples"]

RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "python:3.9.12-slim-buster" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "build-essential" \
\n ] \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n "glmsingle", \
\n "setup.py", \
\n "MANIFEST.in", \
\n "README.md", \
\n "requirements.txt", \
\n "/glmsingle/" \
\n ] \
\n ], \
\n [ \
\n "workdir", \
\n "/glmsingle" \
\n ], \
\n [ \
\n "run", \
\n "pip install ." \
\n ], \
\n [ \
\n "user", \
\n "neuro" \
\n ], \
\n [ \
\n "workdir", \
\n "/home/neuro" \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n "examples", \
\n "/home/neuro/examples" \
\n ] \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
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