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Build an nipype docker image based on neurodocker
#!/bin/bash
# Note that this repo includes a Singularity file too
git clone https://github.com/miykael/nipype_tutorial
cd nipype_tutorial
chmod +x generate.sh
./generate.sh
docker build --tag jjnipype .
./run_nipype_tutorial_docker
#!/bin/bash
git clone https://github.com/ReproNim/neurodocker
cd neurodocker
python3 -m pip install --no-cache-dir --editable '.[all]'
# In the event of importlib_metadata errors:
# python3 -m pip uninstall importlib_metadata
# python3 -m pip install importlib_metadata
# then try installing again
#!/bin/bash
# Paths are specific to my system, but should be a
# good example.
source /usr/local/Caskroom/miniconda/base/etc/profile.d/conda.sh
conda activate nipype
docker run -it --rm \
-v /Volumes/Data/Research/fmri/fmri_rs/code/:/home/neuro/nipype_tutorial \
-v /Volumes/Data/Research/fmri/fmri_rs/:/data \
-v /Volumes/Data/Research/fmri/fmri_rs/derivatives/output/:/output \
-p 8888:8888 \
jjnipype \
jupyter notebook
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