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djareckadjarecka
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updating python and adding niflow.nipype1 to the requirements
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‎Dockerfile

Lines changed: 33 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
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# Generated by Neurodocker version 0.5.0
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# Timestamp: 2019-07-14 08:54:07 UTC
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# Your version: 0.6.0+5.g74cb187.dirty Latest version: 0.7.0
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# Generated by Neurodocker version 0.6.0+5.g74cb187.dirty
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# Timestamp: 2020-08-05 04:01:42 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
@@ -9,6 +10,8 @@
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1011
FROM neurodebian:stretch-non-free
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13+
USER root
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1215
ARG DEBIAN_FRONTEND="noninteractive"
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ENV LANG="en_US.UTF-8" \
@@ -91,12 +94,12 @@ RUN export TMPDIR="$(mktemp -d)" \
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&& rm -rf "$TMPDIR" \
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&& unset TMPDIR \
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&& echo "Downloading standalone SPM ..." \
94-
&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
97+
&& curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
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&& unzip -q /tmp/spm12.zip -d /tmp \
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&& mkdir -p /opt/spm12-r7219 \
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&& mv /tmp/spm12/* /opt/spm12-r7219/ \
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&& chmod -R 777 /opt/spm12-r7219 \
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&& rm -rf /tmp/* \
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&& rm -rf /tmp/spm* \
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&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
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&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
102105

@@ -120,35 +123,35 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
120123
&& sync && conda clean --all && sync \
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&& conda create -y -q --name neuro \
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&& conda install -y -q --name neuro \
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'python=3.6' \
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'pytest' \
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'jupyter' \
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'jupyterlab' \
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'jupyter_contrib_nbextensions' \
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'traits' \
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'pandas' \
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'matplotlib' \
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'scikit-learn' \
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'scikit-image' \
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'seaborn' \
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'nbformat' \
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'nb_conda' \
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"python=3.7" \
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"pytest" \
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"jupyter" \
129+
"jupyterlab" \
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"jupyter_contrib_nbextensions" \
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"traits" \
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"pandas" \
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"matplotlib" \
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"scikit-learn" \
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"scikit-image" \
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"seaborn" \
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"nbformat" \
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"nb_conda" \
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&& sync && conda clean --all && sync \
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&& bash -c "source activate neuro \
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&& pip install --no-cache-dir \
139-
https://github.com/nipy/nipype/tarball/master \
140-
https://github.com/INCF/pybids/tarball/0.7.1 \
141-
niflow-nipype1-workflows \
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nilearn \
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datalad[full] \
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nipy \
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duecredit \
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nbval" \
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"https://github.com/nipy/nipype/tarball/master" \
143+
"https://github.com/INCF/pybids/tarball/0.7.1" \
144+
"nilearn" \
145+
"datalad[full]" \
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"nipy" \
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"duecredit" \
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"nbval" \
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"niflow-nipype1-workflows"" \
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&& rm -rf ~/.cache/pip/* \
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&& sync \
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&& sed -i '$isource activate neuro' $ND_ENTRYPOINT
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151-
ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0"
154+
ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:"
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RUN bash -c 'source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main'
154157

@@ -232,9 +235,8 @@ RUN echo '{ \
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\n [ \
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\n "miniconda", \
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\n { \
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\n "miniconda_version": "4.3.31", \
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\n "conda_install": [ \
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\n "python=3.6", \
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\n "python=3.7", \
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\n "pytest", \
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\n "jupyter", \
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\n "jupyterlab", \
@@ -255,7 +257,8 @@ RUN echo '{ \
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\n "datalad[full]", \
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\n "nipy", \
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\n "duecredit", \
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\n "nbval" \
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\n "nbval", \
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\n "niflow-nipype1-workflows" \
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\n ], \
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\n "create_env": "neuro", \
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\n "activate": true \
@@ -264,7 +267,7 @@ RUN echo '{ \
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\n [ \
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\n "env", \
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\n { \
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\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0" \
270+
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:" \
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\n } \
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\n ], \
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\n [ \

‎Singularity

Lines changed: 37 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
1-
# Generated by Neurodocker version 0.5.0
2-
# Timestamp: 2019-07-14 08:54:09 UTC
1+
# Your version: 0.6.0+5.g74cb187.dirty Latest version: 0.7.0
2+
# Generated by Neurodocker version 0.6.0+5.g74cb187.dirty
3+
# Timestamp: 2020-08-05 04:01:43 UTC
34
#
45
# Thank you for using Neurodocker. If you discover any issues
56
# or ways to improve this software, please submit an issue or
@@ -11,6 +12,8 @@ Bootstrap: docker
1112
From: neurodebian:stretch-non-free
1213

1314
%post
15+
su - root
16+
1417
export ND_ENTRYPOINT="/neurodocker/startup.sh"
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apt-get update -qq
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apt-get install -y -q --no-install-recommends \
@@ -83,12 +86,12 @@ chmod +x "$TMPDIR/MCRInstaller.bin"
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rm -rf "$TMPDIR"
8487
unset TMPDIR
8588
echo "Downloading standalone SPM ..."
86-
curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
89+
curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
8790
unzip -q /tmp/spm12.zip -d /tmp
8891
mkdir -p /opt/spm12-r7219
8992
mv /tmp/spm12/* /opt/spm12-r7219/
9093
chmod -R 777 /opt/spm12-r7219
91-
rm -rf /tmp/*
94+
rm -rf /tmp/spm*
9295
/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
9396
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
9497

@@ -110,29 +113,30 @@ conda config --system --set show_channel_urls true
110113
sync && conda clean --all && sync
111114
conda create -y -q --name neuro
112115
conda install -y -q --name neuro \
113-
'python=3.6' \
114-
'pytest' \
115-
'jupyter' \
116-
'jupyterlab' \
117-
'jupyter_contrib_nbextensions' \
118-
'traits' \
119-
'pandas' \
120-
'matplotlib' \
121-
'scikit-learn' \
122-
'scikit-image' \
123-
'seaborn' \
124-
'nbformat' \
125-
'nb_conda'
116+
"python=3.7" \
117+
"pytest" \
118+
"jupyter" \
119+
"jupyterlab" \
120+
"jupyter_contrib_nbextensions" \
121+
"traits" \
122+
"pandas" \
123+
"matplotlib" \
124+
"scikit-learn" \
125+
"scikit-image" \
126+
"seaborn" \
127+
"nbformat" \
128+
"nb_conda"
126129
sync && conda clean --all && sync
127130
bash -c "source activate neuro
128131
pip install --no-cache-dir \
129-
https://github.com/nipy/nipype/tarball/master \
130-
https://github.com/INCF/pybids/tarball/0.7.1 \
131-
nilearn \
132-
datalad[full] \
133-
nipy \
134-
duecredit \
135-
nbval"
132+
"https://github.com/nipy/nipype/tarball/master" \
133+
"https://github.com/INCF/pybids/tarball/0.7.1" \
134+
"nilearn" \
135+
"datalad[full]" \
136+
"nipy" \
137+
"duecredit" \
138+
"nbval" \
139+
"niflow-nipype1-workflows""
136140
rm -rf ~/.cache/pip/*
137141
sync
138142
sed -i '$isource activate neuro' $ND_ENTRYPOINT
@@ -174,6 +178,10 @@ echo '{
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\n "neurodebian:stretch-non-free"
175179
\n ],
176180
\n [
181+
\n "user",
182+
\n "root"
183+
\n ],
184+
\n [
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\n "_header",
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\n {
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\n "version": "generic",
@@ -223,9 +231,8 @@ echo '{
223231
\n [
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\n "miniconda",
225233
\n {
226-
\n "miniconda_version": "4.3.31",
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\n "conda_install": [
228-
\n "python=3.6",
235+
\n "python=3.7",
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\n "pytest",
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\n "jupyter",
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\n "jupyterlab",
@@ -246,7 +253,8 @@ echo '{
246253
\n "datalad[full]",
247254
\n "nipy",
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\n "duecredit",
249-
\n "nbval"
256+
\n "nbval",
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\n "niflow-nipype1-workflows"
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\n ],
251259
\n "create_env": "neuro",
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\n "activate": true
@@ -255,7 +263,7 @@ echo '{
255263
\n [
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\n "env",
257265
\n {
258-
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0"
266+
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:"
259267
\n }
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\n ],
261269
\n [
@@ -333,7 +341,7 @@ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmc
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export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
334342
export CONDA_DIR="/opt/miniconda-latest"
335343
export PATH="/opt/miniconda-latest/bin:$PATH"
336-
export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:/usr/lib/fsl/5.0"
344+
export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:"
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338346
%files
339347
. /home/neuro/nipype_tutorial

‎generate.sh

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -14,12 +14,12 @@ generate_docker() {
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--spm12 version=r7219 \
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--user=neuro \
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--workdir /home/neuro \
17-
--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
17+
--miniconda \
18+
conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions
1919
traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
2020
pip_install="https://github.com/nipy/nipype/tarball/master
2121
https://github.com/INCF/pybids/tarball/0.7.1
22-
nilearn datalad[full] nipy duecredit nbval" \
22+
nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \
2323
create_env="neuro" \
2424
activate=True \
2525
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:$LD_LIBRARY_PATH" \
@@ -53,12 +53,12 @@ generate_singularity() {
5353
--spm12 version=r7219 \
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--user=neuro \
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--workdir /home/neuro \
56-
--miniconda miniconda_version="4.3.31" \
57-
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
56+
--miniconda \
57+
conda_install="python=3.7 pytest jupyter jupyterlab jupyter_contrib_nbextensions
5858
traits pandas matplotlib scikit-learn scikit-image seaborn nbformat nb_conda" \
5959
pip_install="https://github.com/nipy/nipype/tarball/master
6060
https://github.com/INCF/pybids/tarball/0.7.1
61-
nilearn datalad[full] nipy duecredit nbval" \
61+
nilearn datalad[full] nipy duecredit nbval niflow-nipype1-workflows" \
6262
create_env="neuro" \
6363
activate=True \
6464
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:$LD_LIBRARY_PATH" \

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