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Merge branch 'master' of https://github.com/ReproNim/reproin
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DBIC BIDS Team committed Sep 3, 2020
2 parents e0fafa7 + a65b113 commit 1d10bf5
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86 changes: 44 additions & 42 deletions Dockerfile
View file
@@ -1,20 +1,22 @@
# 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
# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2020/05/04 15:32:19 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
# https://github.com/ReproNim/neurodocker

FROM neurodebian:buster

USER root

ARG DEBIAN_FRONTEND="noninteractive"

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends neurodebian-freeze \
&& nd_freeze 20191217 \
&& nd_freeze 20200503 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

Expand Down Expand Up @@ -59,30 +61,33 @@ RUN apt-get update -qq \
procps \
datalad \
pigz \
less \
tree \
git-annex-standalone \
python-nipype \
python-nibabel \
python3-nipype \
virtualenv \
python-dcmstack \
python-configparser \
python-funcsigs \
python-pytest \
shellcheck \
python3-dcmstack \
python3-funcsigs \
python3-etelemetry \
python3-pytest \
dcmtk \
python-pip \
python-wheel \
python-setuptools \
python-datalad \
python-filelock \
python3-pip \
python3-wheel \
python3-setuptools \
python3-datalad \
python3-filelock \
dcm2niix \
python-pytest \
python3-pytest \
python3-nose \
heudiconv \
heudiconv=0.8.0-2~nd100+1 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

RUN :

RUN curl -sL https://deb.nodesource.com/setup_6.x | bash -
RUN curl -sL https://deb.nodesource.com/setup_9.x | bash -

RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
Expand All @@ -91,16 +96,14 @@ RUN apt-get update -qq \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*

RUN npm install -g bids-validator@1.3.12
RUN npm install -g bids-validator@1.5.1

RUN mkdir /afs /inbox

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

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

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

RUN echo '{ \
\n "pkg_manager": "apt", \
Expand All @@ -112,7 +115,7 @@ RUN echo '{ \
\n [ \
\n "ndfreeze", \
\n { \
\n "date": "20191217" \
\n "date": "20200503" \
\n } \
\n ], \
\n [ \
Expand All @@ -128,24 +131,27 @@ RUN echo '{ \
\n "procps", \
\n "datalad", \
\n "pigz", \
\n "less", \
\n "tree", \
\n "git-annex-standalone", \
\n "python-nipype", \
\n "python-nibabel", \
\n "python3-nipype", \
\n "virtualenv", \
\n "python-dcmstack", \
\n "python-configparser", \
\n "python-funcsigs", \
\n "python-pytest", \
\n "shellcheck", \
\n "python3-dcmstack", \
\n "python3-funcsigs", \
\n "python3-etelemetry", \
\n "python3-pytest", \
\n "dcmtk", \
\n "python-pip", \
\n "python-wheel", \
\n "python-setuptools", \
\n "python-datalad", \
\n "python-filelock", \
\n "python3-pip", \
\n "python3-wheel", \
\n "python3-setuptools", \
\n "python3-datalad", \
\n "python3-filelock", \
\n "dcm2niix", \
\n "python-pytest", \
\n "python3-pytest", \
\n "python3-nose", \
\n "heudiconv" \
\n "heudiconv=0.8.0-2~nd100+1" \
\n ] \
\n ], \
\n [ \
Expand All @@ -154,7 +160,7 @@ RUN echo '{ \
\n ], \
\n [ \
\n "run", \
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - " \
\n "curl -sL https://deb.nodesource.com/setup_9.x | bash - " \
\n ], \
\n [ \
\n "install", \
Expand All @@ -165,23 +171,19 @@ RUN echo '{ \
\n ], \
\n [ \
\n "run", \
\n "npm install -g bids-validator@1.3.12" \
\n "npm install -g bids-validator@1.5.1" \
\n ], \
\n [ \
\n "run", \
\n "mkdir /afs /inbox" \
\n ], \
\n [ \
\n "run", \
\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 "/usr/bin/heudiconv" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
5 changes: 2 additions & 3 deletions README.md
View file
Expand Up @@ -53,9 +53,8 @@ heuristic
`apt-get update; apt-get install heudiconv datalad` in any NeuroDebian environment.
If you do not have one, you could get either of
- [NeuroDebian Virtual Machine](http://neuro.debian.net/vm.html)
- Docker image: `docker run -it --rm -v $PWD:$PWD neurodebian`
- Singularity image (big but useful), comes with heudiconv and
datalad preinstalled: `singularity pull shub://neurodebian/neurodebian`
- ReproIn Docker image: `docker run -it --rm -v $PWD:$PWD repronim/reproin`
- ReproIn Singularity image: `singularity pull shub://ReproNim/reproin`

2. Collect a subject/session (or multiple of them) while placing and
naming sequences in the scanner following the [specification].
Expand Down
90 changes: 48 additions & 42 deletions Singularity
View file
@@ -1,23 +1,25 @@
# 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
# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
# Latest release: Neurodocker version 0.7.0
# Timestamp: 2020/05/04 15:32:21 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
# https://github.com/ReproNim/neurodocker

Bootstrap: docker
From: neurodebian:buster

%post
apt-get update -qq
apt-get install -y -q --no-install-recommends neurodebian-freeze
nd_freeze 20191217
nd_freeze 20200503
apt-get clean
rm -rf /var/lib/apt/lists/*

su - root

export ND_ENTRYPOINT="/neurodocker/startup.sh"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
Expand Down Expand Up @@ -54,30 +56,33 @@ apt-get install -y -q --no-install-recommends \
procps \
datalad \
pigz \
less \
tree \
git-annex-standalone \
python-nipype \
python-nibabel \
python3-nipype \
virtualenv \
python-dcmstack \
python-configparser \
python-funcsigs \
python-pytest \
shellcheck \
python3-dcmstack \
python3-funcsigs \
python3-etelemetry \
python3-pytest \
dcmtk \
python-pip \
python-wheel \
python-setuptools \
python-datalad \
python-filelock \
python3-pip \
python3-wheel \
python3-setuptools \
python3-datalad \
python3-filelock \
dcm2niix \
python-pytest \
python3-pytest \
python3-nose \
heudiconv
heudiconv=0.8.0-2~nd100+1
apt-get clean
rm -rf /var/lib/apt/lists/*

:

curl -sL https://deb.nodesource.com/setup_6.x | bash -
curl -sL https://deb.nodesource.com/setup_9.x | bash -

apt-get update -qq
apt-get install -y -q --no-install-recommends \
Expand All @@ -86,12 +91,10 @@ apt-get install -y -q --no-install-recommends \
apt-get clean
rm -rf /var/lib/apt/lists/*

npm install -g bids-validator@1.3.12
npm install -g bids-validator@1.5.1

mkdir /afs /inbox

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

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

Expand All @@ -105,10 +108,14 @@ echo '{
\n [
\n "ndfreeze",
\n {
\n "date": "20191217"
\n "date": "20200503"
\n }
\n ],
\n [
\n "user",
\n "root"
\n ],
\n [
\n "_header",
\n {
\n "version": "generic",
Expand All @@ -128,24 +135,27 @@ echo '{
\n "procps",
\n "datalad",
\n "pigz",
\n "less",
\n "tree",
\n "git-annex-standalone",
\n "python-nipype",
\n "python-nibabel",
\n "python3-nipype",
\n "virtualenv",
\n "python-dcmstack",
\n "python-configparser",
\n "python-funcsigs",
\n "python-pytest",
\n "shellcheck",
\n "python3-dcmstack",
\n "python3-funcsigs",
\n "python3-etelemetry",
\n "python3-pytest",
\n "dcmtk",
\n "python-pip",
\n "python-wheel",
\n "python-setuptools",
\n "python-datalad",
\n "python-filelock",
\n "python3-pip",
\n "python3-wheel",
\n "python3-setuptools",
\n "python3-datalad",
\n "python3-filelock",
\n "dcm2niix",
\n "python-pytest",
\n "python3-pytest",
\n "python3-nose",
\n "heudiconv"
\n "heudiconv=0.8.0-2~nd100+1"
\n ]
\n ],
\n [
Expand All @@ -154,7 +164,7 @@ echo '{
\n ],
\n [
\n "run",
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - "
\n "curl -sL https://deb.nodesource.com/setup_9.x | bash - "
\n ],
\n [
\n "install",
Expand All @@ -165,23 +175,19 @@ echo '{
\n ],
\n [
\n "run",
\n "npm install -g bids-validator@1.3.12"
\n "npm install -g bids-validator@1.5.1"
\n ],
\n [
\n "run",
\n "mkdir /afs /inbox"
\n ],
\n [
\n "run",
\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 "/usr/bin/heudiconv \"$@\""
\n ]
\n ]
\n}' > /neurodocker/neurodocker_specs.json
Expand All @@ -192,4 +198,4 @@ export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"

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

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