MNT: Use .neurodocker.json for neurodocker.sh

docker/neurodocker.sh

@@ -1,47 +1,4 @@
-neurodocker generate docker \
-  --pkg-manager apt \
-  --base neurodebian:stretch \
-  --arg DEBIAN_FRONTEND=noninteractive \
-  --label maintainer="Shashank Bansal" \
-  --env MKL_NUM_THREADS="1" OMP_NUM_THREADS="1" \
-  --install apt-utils unzip curl graphviz \
-          wget git-annex-standalone git vim \
-          tig git-annex-remote-rclone \
-  --user neuro \
-  --workdir "/home/neuro" \
-  --miniconda version=latest create_env=neuro \
-  conda_install="python=3.9 numpy pytest
-                  traits pandas matplotlib
-		  scikit-learn scikit-image
-		  seaborn nbformat nb_conda" \
-  --run 'conda install -y --channel leej3 --name neuro "afni-minimal" && sync && conda clean -y --all && sync' \
-  --copy . "/src/fitlins" \
-  --user  root \
-  --run 'mkdir /work && chown -R neuro /src /work && chmod a+w /work' \
-  --user neuro \
-  --arg VERSION \
-  --run 'echo "$VERSION" > /src/fitlins/VERSION' \
-  --run 'sed -i -e '"'"'s/crashfile_format = pklz/crashfile_format = txt/'"'"' /src/fitlins/fitlins/data/nipype.cfg' \
-  --run-bash 'source activate neuro \
-      && pip install --no-cache-dir -r /src/fitlins/requirements.txt \
-      && rm -rf ~/.cache/pip/* \
-      && sync \
-      && sed -i "$isource activate neuro" $ND_ENTRYPOINT' \
-  --run-bash 'source activate neuro \
-      && pip install --no-cache-dir  \
-      "/src/fitlins[all]" \
-      && rm -rf ~/.cache/pip/* \
-      && sync \
-      && sed -i "$isource activate neuro" $ND_ENTRYPOINT' \
-  --workdir "/work" \
-  --entrypoint "/neurodocker/startup.sh fitlins" \
-  --arg BUILD_DATE \
-  --arg VCS_REF \
-  --label org.label-schema.build-date='$BUILD_DATE' \
-      org.label-schema.name="FitLins" \
-      org.label-schema.description="FitLins - Fit Linear Models to BIDS datasets" \
-      org.label-schema.url="http://github.com/poldracklab/fitlins" \
-      org.label-schema.vcs-ref='$VCS_REF' \
-      org.label-schema.vcs-url="https://github.com/poldracklab/fitlins" \
-      org.label-schema.version='$VERSION' \
-      org.label-schema.schema-version="1.0"  > Dockerfile
+#!/bin/bash
+
+docker run --rm -i -a stdin -a stdout \
+  repronim/neurodocker:0.7.0 generate docker - < .neurodocker.json > Dockerfile