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[DATALAD RUNCMD] ./generate_container.sh
=== Do not change lines below === { "chain": [ "ba60d86cdfa7f535bb4c9cb5f20651dda00107e0" ], "cmd": "./generate_container.sh", "exit": 0, "inputs": [], "outputs": [ "Singularity*", "Dockerfile" ], "pwd": "." } ^^^ Do not change lines above ^^^
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‎Dockerfile

Lines changed: 8 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Generated by Neurodocker version 0.4.3-2-g01cdd22
2-
# Timestamp: 2019-01-05 06:19:25 UTC
2+
# Timestamp: 2019-01-12 15:56:46 UTC
33
#
44
# Thank you for using Neurodocker. If you discover any issues
55
# or ways to improve this software, please submit an issue or
@@ -16,7 +16,7 @@ RUN apt-get update -qq \
1616
neurodebian-freeze \
1717
&& apt-get clean \
1818
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
19-
&& nd_freeze 20190105
19+
&& nd_freeze 20190112
2020

2121
ENV LANG="en_US.UTF-8" \
2222
LC_ALL="en_US.UTF-8" \
@@ -70,6 +70,8 @@ RUN apt-get update -qq \
7070
python-wheel \
7171
python-setuptools \
7272
python-datalad \
73+
heudiconv \
74+
dcm2niix \
7375
&& apt-get clean \
7476
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
7577

@@ -86,31 +88,6 @@ RUN npm install -g [email protected]
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8789
RUN mkdir /afs /inbox
8890

89-
RUN pip install heudiconv
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91-
ENV PATH="/opt/dcm2niix-v1.0.20181125/bin:$PATH"
92-
RUN apt-get update -qq \
93-
&& apt-get install -y -q --no-install-recommends \
94-
cmake \
95-
g++ \
96-
gcc \
97-
git \
98-
make \
99-
pigz \
100-
zlib1g-dev \
101-
&& apt-get clean \
102-
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
103-
&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
104-
&& cd /tmp/dcm2niix \
105-
&& git fetch --tags \
106-
&& git checkout v1.0.20181125 \
107-
&& mkdir /tmp/dcm2niix/build \
108-
&& cd /tmp/dcm2niix/build \
109-
&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20181125 .. \
110-
&& make \
111-
&& make install \
112-
&& rm -rf /tmp/dcm2niix
113-
11491
RUN echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
11592

11693
RUN useradd --no-user-group --create-home --shell /bin/bash reproin
@@ -128,7 +105,7 @@ RUN echo '{ \
128105
\n [ \
129106
\n "ndfreeze", \
130107
\n { \
131-
\n "date": "20190105" \
108+
\n "date": "20190112" \
132109
\n } \
133110
\n ], \
134111
\n [ \
@@ -155,7 +132,9 @@ RUN echo '{ \
155132
\n "python-pip", \
156133
\n "python-wheel", \
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\n "python-setuptools", \
158-
\n "python-datalad" \
135+
\n "python-datalad", \
136+
\n "heudiconv", \
137+
\n "dcm2niix" \
159138
\n ] \
160139
\n ], \
161140
\n [ \
@@ -179,17 +158,6 @@ RUN echo '{ \
179158
\n ], \
180159
\n [ \
181160
\n "run", \
182-
\n "pip install heudiconv" \
183-
\n ], \
184-
\n [ \
185-
\n "dcm2niix", \
186-
\n { \
187-
\n "version": "v1.0.20181125", \
188-
\n "method": "source" \
189-
\n } \
190-
\n ], \
191-
\n [ \
192-
\n "run", \
193161
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh" \
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\n ], \
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\n [ \

‎Singularity

Lines changed: 9 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Generated by Neurodocker version 0.4.3-2-g01cdd22
2-
# Timestamp: 2019-01-05 06:19:26 UTC
2+
# Timestamp: 2019-01-12 15:56:47 UTC
33
#
44
# Thank you for using Neurodocker. If you discover any issues
55
# or ways to improve this software, please submit an issue or
@@ -16,7 +16,7 @@ apt-get install -y -q --no-install-recommends \
1616
neurodebian-freeze
1717
apt-get clean
1818
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
19-
nd_freeze 20190105
19+
nd_freeze 20190112
2020

2121
export ND_ENTRYPOINT="/neurodocker/startup.sh"
2222
apt-get update -qq
@@ -64,7 +64,9 @@ apt-get install -y -q --no-install-recommends \
6464
python-pip \
6565
python-wheel \
6666
python-setuptools \
67-
python-datalad
67+
python-datalad \
68+
heudiconv \
69+
dcm2niix
6870
apt-get clean
6971
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
7072

@@ -81,30 +83,6 @@ npm install -g [email protected]
8183

8284
mkdir /afs /inbox
8385

84-
pip install heudiconv
85-
86-
apt-get update -qq
87-
apt-get install -y -q --no-install-recommends \
88-
cmake \
89-
g++ \
90-
gcc \
91-
git \
92-
make \
93-
pigz \
94-
zlib1g-dev
95-
apt-get clean
96-
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
97-
git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix
98-
cd /tmp/dcm2niix
99-
git fetch --tags
100-
git checkout v1.0.20181125
101-
mkdir /tmp/dcm2niix/build
102-
cd /tmp/dcm2niix/build
103-
cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20181125 ..
104-
make
105-
make install
106-
rm -rf /tmp/dcm2niix
107-
10886
echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
10987

11088
useradd --no-user-group --create-home --shell /bin/bash reproin
@@ -120,7 +98,7 @@ echo '{
12098
\n [
12199
\n "ndfreeze",
122100
\n {
123-
\n "date": "20190105"
101+
\n "date": "20190112"
124102
\n }
125103
\n ],
126104
\n [
@@ -154,7 +132,9 @@ echo '{
154132
\n "python-pip",
155133
\n "python-wheel",
156134
\n "python-setuptools",
157-
\n "python-datalad"
135+
\n "python-datalad",
136+
\n "heudiconv",
137+
\n "dcm2niix"
158138
\n ]
159139
\n ],
160140
\n [
@@ -178,17 +158,6 @@ echo '{
178158
\n ],
179159
\n [
180160
\n "run",
181-
\n "pip install heudiconv"
182-
\n ],
183-
\n [
184-
\n "dcm2niix",
185-
\n {
186-
\n "version": "v1.0.20181125",
187-
\n "method": "source"
188-
\n }
189-
\n ],
190-
\n [
191-
\n "run",
192161
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
193162
\n ],
194163
\n [
@@ -206,7 +175,6 @@ echo '{
206175
export LANG="en_US.UTF-8"
207176
export LC_ALL="en_US.UTF-8"
208177
export ND_ENTRYPOINT="/neurodocker/startup.sh"
209-
export PATH="/opt/dcm2niix-v1.0.20181125/bin:$PATH"
210178

211179
%runscript
212180
/neurodocker/heudiconv.sh

‎Singularity.0.5.3

Lines changed: 180 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,180 @@
1+
# Generated by Neurodocker version 0.4.3-2-g01cdd22
2+
# Timestamp: 2019-01-12 15:56:47 UTC
3+
#
4+
# Thank you for using Neurodocker. If you discover any issues
5+
# or ways to improve this software, please submit an issue or
6+
# pull request on our GitHub repository:
7+
#
8+
# https://github.com/kaczmarj/neurodocker
9+
10+
Bootstrap: docker
11+
From: neurodebian:stretch
12+
13+
%post
14+
apt-get update -qq
15+
apt-get install -y -q --no-install-recommends \
16+
neurodebian-freeze
17+
apt-get clean
18+
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
19+
nd_freeze 20190112
20+
21+
export ND_ENTRYPOINT="/neurodocker/startup.sh"
22+
apt-get update -qq
23+
apt-get install -y -q --no-install-recommends \
24+
apt-utils \
25+
bzip2 \
26+
ca-certificates \
27+
curl \
28+
locales \
29+
unzip
30+
apt-get clean
31+
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
32+
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
33+
dpkg-reconfigure --frontend=noninteractive locales
34+
update-locale LANG="en_US.UTF-8"
35+
chmod 777 /opt && chmod a+s /opt
36+
mkdir -p /neurodocker
37+
if [ ! -f "$ND_ENTRYPOINT" ]; then
38+
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
39+
echo 'set -e' >> "$ND_ENTRYPOINT"
40+
echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
41+
fi
42+
chmod -R 777 /neurodocker && chmod a+s /neurodocker
43+
44+
apt-get update -qq
45+
apt-get install -y -q --no-install-recommends \
46+
vim \
47+
wget \
48+
strace \
49+
time \
50+
ncdu \
51+
gnupg \
52+
curl \
53+
procps \
54+
datalad \
55+
pigz \
56+
git-annex-standalone \
57+
python-nipype \
58+
virtualenv \
59+
python-dcmstack \
60+
python-configparser \
61+
python-funcsigs \
62+
python-pytest \
63+
dcmtk \
64+
python-pip \
65+
python-wheel \
66+
python-setuptools \
67+
python-datalad \
68+
heudiconv \
69+
dcm2niix
70+
apt-get clean
71+
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
72+
73+
curl -sL https://deb.nodesource.com/setup_6.x | bash -
74+
75+
apt-get update -qq
76+
apt-get install -y -q --no-install-recommends \
77+
nodejs \
78+
npm
79+
apt-get clean
80+
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
81+
82+
npm install -g [email protected]
83+
84+
mkdir /afs /inbox
85+
86+
echo '#!/bin/bash' >> /neurodocker/heudiconv.sh && echo 'heudiconv "$@"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh
87+
88+
useradd --no-user-group --create-home --shell /bin/bash reproin
89+
su - reproin
90+
91+
echo '{
92+
\n "pkg_manager": "apt",
93+
\n "instructions": [
94+
\n [
95+
\n "base",
96+
\n "neurodebian:stretch"
97+
\n ],
98+
\n [
99+
\n "ndfreeze",
100+
\n {
101+
\n "date": "20190112"
102+
\n }
103+
\n ],
104+
\n [
105+
\n "_header",
106+
\n {
107+
\n "version": "generic",
108+
\n "method": "custom"
109+
\n }
110+
\n ],
111+
\n [
112+
\n "install",
113+
\n [
114+
\n "vim",
115+
\n "wget",
116+
\n "strace",
117+
\n "time",
118+
\n "ncdu",
119+
\n "gnupg",
120+
\n "curl",
121+
\n "procps",
122+
\n "datalad",
123+
\n "pigz",
124+
\n "git-annex-standalone",
125+
\n "python-nipype",
126+
\n "virtualenv",
127+
\n "python-dcmstack",
128+
\n "python-configparser",
129+
\n "python-funcsigs",
130+
\n "python-pytest",
131+
\n "dcmtk",
132+
\n "python-pip",
133+
\n "python-wheel",
134+
\n "python-setuptools",
135+
\n "python-datalad",
136+
\n "heudiconv",
137+
\n "dcm2niix"
138+
\n ]
139+
\n ],
140+
\n [
141+
\n "run",
142+
\n "curl -sL https://deb.nodesource.com/setup_6.x | bash - "
143+
\n ],
144+
\n [
145+
\n "install",
146+
\n [
147+
\n "nodejs",
148+
\n "npm"
149+
\n ]
150+
\n ],
151+
\n [
152+
\n "run",
153+
\n "npm install -g [email protected]"
154+
\n ],
155+
\n [
156+
\n "run",
157+
\n "mkdir /afs /inbox"
158+
\n ],
159+
\n [
160+
\n "run",
161+
\n "echo '"'"'#!/bin/bash'"'"' >> /neurodocker/heudiconv.sh && echo '"'"'heudiconv \"$@\"'"'"' >> /neurodocker/heudiconv.sh && chmod +x /neurodocker/heudiconv.sh"
162+
\n ],
163+
\n [
164+
\n "user",
165+
\n "reproin"
166+
\n ],
167+
\n [
168+
\n "entrypoint",
169+
\n "/neurodocker/heudiconv.sh"
170+
\n ]
171+
\n ]
172+
\n}' > /neurodocker/neurodocker_specs.json
173+
174+
%environment
175+
export LANG="en_US.UTF-8"
176+
export LC_ALL="en_US.UTF-8"
177+
export ND_ENTRYPOINT="/neurodocker/startup.sh"
178+
179+
%runscript
180+
/neurodocker/heudiconv.sh

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