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[DATALAD RUNCMD] ./generate_container.sh

=== Do not change lines below ===
{
 "chain": [
  "ba60d86cdfa7f535bb4c9cb5f20651dda00107e0",
  "1f2f1c17601dae0068bb205587e0d86a776a169e",
  "6464fbb1555170edb3ae6857fb325e2a9924966c"
 ],
 "cmd": "./generate_container.sh",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [
  "Singularity*",
  "Dockerfile"
 ],
 "pwd": "."
}
^^^ Do not change lines above ^^^
  • Loading branch information
yarikoptic committed Dec 19, 2019
1 parent f43063e commit 86ba132e0e8f1107d76c570a506feb1781adb0d2
Showing with 266 additions and 45 deletions.
  1. +35 −22 Dockerfile
  2. +36 −23 Singularity
  3. +195 −0 Singularity.0.6.0
@@ -1,22 +1,22 @@
# Generated by Neurodocker version 0.4.3-2-g01cdd22
# Timestamp: 2019-05-14 18:40:33 UTC
# Could not check for version updates: Connection to server could not be made
# Generated by Neurodocker version 0.6.0
# Timestamp: 2019-12-19 23:33:25 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/kaczmarj/neurodocker

FROM neurodebian:stretch
FROM neurodebian:buster

ARG DEBIAN_FRONTEND="noninteractive"

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
neurodebian-freeze \
&& apt-get install -y -q --no-install-recommends neurodebian-freeze \
&& nd_freeze 20191217 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& nd_freeze 20190513
&& rm -rf /var/lib/apt/lists/*

ENV LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8" \
@@ -31,7 +31,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
locales \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& 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" \
@@ -40,6 +40,7 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
&& 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
@@ -70,11 +71,16 @@ RUN apt-get update -qq \
python-wheel \
python-setuptools \
python-datalad \
heudiconv \
python-filelock \
dcm2niix \
python-pytest \
python3-pytest \
python3-nose \
heudiconv \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
&& rm -rf /var/lib/apt/lists/*

RUN :

RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -

@@ -83,30 +89,30 @@ RUN apt-get update -qq \
nodejs \
npm \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
&& rm -rf /var/lib/apt/lists/*

RUN npm install -g bids-validator@1.1.1
RUN npm install -g bids-validator@1.3.12

RUN mkdir /afs /inbox

RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'set -eu; heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh

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

ENTRYPOINT ["/neurodocker/heudiconv.sh"]
ENTRYPOINT ["/neurodocker/heudiconv.sh", "\"$@\""]

RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch" \
\n "neurodebian:buster" \
\n ], \
\n [ \
\n "ndfreeze", \
\n { \
\n "date": "20190513" \
\n "date": "20191217" \
\n } \
\n ], \
\n [ \
@@ -134,13 +140,20 @@ RUN echo '{ \
\n "python-wheel", \
\n "python-setuptools", \
\n "python-datalad", \
\n "heudiconv", \
\n "python-filelock", \
\n "dcm2niix", \
\n "python-pytest" \
\n "python-pytest", \
\n "python3-pytest", \
\n "python3-nose", \
\n "heudiconv" \
\n ] \
\n ], \
\n [ \
\n "run", \
\n ":" \
\n ], \
\n [ \
\n "run", \
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - " \
\n ], \
\n [ \
@@ -152,23 +165,23 @@ RUN echo '{ \
\n ], \
\n [ \
\n "run", \
\n "npm install -g bids-validator@1.1.1" \
\n "npm install -g bids-validator@1.3.12" \
\n ], \
\n [ \
\n "run", \
\n "mkdir /afs /inbox" \
\n ], \
\n [ \
\n "run", \
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'set -eu; heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
\n ], \
\n [ \
\n "user", \
\n "reproin" \
\n ], \
\n [ \
\n "entrypoint", \
\n "/neurodocker/heudiconv.sh" \
\n "/neurodocker/heudiconv.sh \"$@\"" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
@@ -1,5 +1,6 @@
# Generated by Neurodocker version 0.4.3-2-g01cdd22
# Timestamp: 2019-05-14 18:40:34 UTC
# Could not check for version updates: Connection to server could not be made
# Generated by Neurodocker version 0.6.0
# Timestamp: 2019-12-19 23:33:31 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
@@ -8,15 +9,14 @@
# https://github.com/kaczmarj/neurodocker

Bootstrap: docker
From: neurodebian:stretch
From: neurodebian:buster

%post
apt-get update -qq
apt-get install -y -q --no-install-recommends \
neurodebian-freeze
apt-get install -y -q --no-install-recommends neurodebian-freeze
nd_freeze 20191217
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
nd_freeze 20190513
rm -rf /var/lib/apt/lists/*

export ND_ENTRYPOINT="/neurodocker/startup.sh"
apt-get update -qq
@@ -28,7 +28,7 @@ apt-get install -y -q --no-install-recommends \
locales \
unzip
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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"
@@ -37,6 +37,7 @@ 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
@@ -65,11 +66,16 @@ apt-get install -y -q --no-install-recommends \
python-wheel \
python-setuptools \
python-datalad \
heudiconv \
python-filelock \
dcm2niix \
python-pytest
python-pytest \
python3-pytest \
python3-nose \
heudiconv
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
rm -rf /var/lib/apt/lists/*

:

curl -sL https://deb.nodesource.com/setup_6.x | bash -

@@ -78,28 +84,28 @@ apt-get install -y -q --no-install-recommends \
nodejs \
npm
apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
rm -rf /var/lib/apt/lists/*

npm install -g bids-validator@1.1.1
npm install -g bids-validator@1.3.12

mkdir /afs /inbox

echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'set -eu; heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh

useradd --no-user-group --create-home --shell /bin/bash reproin
test "$(getent passwd reproin)" || useradd --no-user-group --create-home --shell /bin/bash reproin
su - reproin

echo '{
\n "pkg_manager": "apt",
\n "instructions": [
\n [
\n "base",
\n "neurodebian:stretch"
\n "neurodebian:buster"
\n ],
\n [
\n "ndfreeze",
\n {
\n "date": "20190513"
\n "date": "20191217"
\n }
\n ],
\n [
@@ -134,13 +140,20 @@ echo '{
\n "python-wheel",
\n "python-setuptools",
\n "python-datalad",
\n "heudiconv",
\n "python-filelock",
\n "dcm2niix",
\n "python-pytest"
\n "python-pytest",
\n "python3-pytest",
\n "python3-nose",
\n "heudiconv"
\n ]
\n ],
\n [
\n "run",
\n ":"
\n ],
\n [
\n "run",
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - "
\n ],
\n [
@@ -152,23 +165,23 @@ echo '{
\n ],
\n [
\n "run",
\n "npm install -g bids-validator@1.1.1"
\n "npm install -g bids-validator@1.3.12"
\n ],
\n [
\n "run",
\n "mkdir /afs /inbox"
\n ],
\n [
\n "run",
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'set -eu; heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
\n ],
\n [
\n "user",
\n "reproin"
\n ],
\n [
\n "entrypoint",
\n "/neurodocker/heudiconv.sh"
\n "/neurodocker/heudiconv.sh \"$@\""
\n ]
\n ]
\n}' > /neurodocker/neurodocker_specs.json
@@ -179,4 +192,4 @@ export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"

%runscript
/neurodocker/heudiconv.sh
/neurodocker/heudiconv.sh "$@"

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