diff --git a/docker/neurodocker.sh b/docker/neurodocker.sh index e1188e1e..7bbb7b39 100755 --- a/docker/neurodocker.sh +++ b/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