/bin/sh -c #(nop) ADD file:40290d9a94ae76c35ab1f57178130ce1c5b976e34a91e77472ecf7e945ab64f9 in /

/bin/sh -c #(nop) CMD ["bash"]

COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg # buildkit

RUN /bin/sh -c apt-get update && apt-get install -y --no-install-recommends apt-utils wget curl bzip2 locales unzip ca-certificates xvfb build-essential autoconf libtool pkg-config graphviz pandoc pandoc-citeproc git && curl -sSL https://deb.nodesource.com/setup_14.x | bash - && apt-get install -y --no-install-recommends nodejs && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # buildkit

ENV FSL_DIR=/usr/share/fsl/5.0 OS=Linux FS_OVERRIDE=0 FIX_VERTEX_AREA= FSF_OUTPUT_FORMAT=nii.gz

RUN /bin/sh -c echo "Downloading C3D ..." && mkdir /opt/c3d && curl -sSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download | tar -xzC /opt/c3d --strip-components=1 # buildkit

ENV C3DPATH=/opt/c3d/bin PATH=/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

RUN /bin/sh -c curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && apt-key add /usr/local/etc/neurodebian.gpg && (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) # buildkit

RUN /bin/sh -c apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends fsl-core=5.0.9-5~nd18.04+1 fsl-mni152-templates=5.0.7-2 afni=18.0.05+git24-gb25b21054~dfsg.1-1~nd17.10+1+nd18.04+1 connectome-workbench=1.5.0-1~nd18.04+1 git-annex-standalone && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # buildkit

RUN /bin/sh -c curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt --exclude='freesurfer/diffusion' --exclude='freesurfer/docs' --exclude='freesurfer/fsfast' --exclude='freesurfer/lib/cuda' --exclude='freesurfer/lib/qt' --exclude='freesurfer/matlab' --exclude='freesurfer/mni/share/man' --exclude='freesurfer/subjects/fsaverage_sym' --exclude='freesurfer/subjects/fsaverage3' --exclude='freesurfer/subjects/fsaverage4' --exclude='freesurfer/subjects/cvs_avg35' --exclude='freesurfer/subjects/cvs_avg35_inMNI152' --exclude='freesurfer/subjects/bert' --exclude='freesurfer/subjects/lh.EC_average' --exclude='freesurfer/subjects/rh.EC_average' --exclude='freesurfer/subjects/sample-*.mgz' --exclude='freesurfer/subjects/V1_average' --exclude='freesurfer/trctrain' # buildkit

ENV FSF_OUTPUT_FORMAT=nii.gz FREESURFER_HOME=/opt/freesurfer

ENV SUBJECTS_DIR=/opt/freesurfer/subjects FUNCTIONALS_DIR=/opt/freesurfer/sessions MNI_DIR=/opt/freesurfer/mni LOCAL_DIR=/opt/freesurfer/local MINC_BIN_DIR=/opt/freesurfer/mni/bin MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DATAPATH=/opt/freesurfer/mni/data

ENV PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 PATH=/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

ENV FSLDIR=/usr/share/fsl/5.0 FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE POSSUMDIR=/usr/share/fsl/5.0 LD_LIBRARY_PATH=/usr/lib/fsl/5.0: FSLTCLSH=/usr/bin/tclsh FSLWISH=/usr/bin/wish AFNI_MODELPATH=/usr/lib/afni/models AFNI_IMSAVE_WARNINGS=NO AFNI_TTATLAS_DATASET=/usr/share/afni/atlases AFNI_PLUGINPATH=/usr/lib/afni/plugins

ENV PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

ENV ANTSPATH=/usr/lib/ants

RUN /bin/sh -c mkdir -p $ANTSPATH && curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | tar -xzC $ANTSPATH --strip-components 1 # buildkit

ENV PATH=/usr/lib/ants:/usr/lib/fsl/5.0:/usr/lib/afni/bin:/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

RUN /bin/sh -c curl -sL https://deb.nodesource.com/setup_14.x | bash - # buildkit

RUN /bin/sh -c apt-get install -y nodejs # buildkit

RUN /bin/sh -c npm install -g svgo # buildkit

RUN /bin/sh -c npm install -g bids-validator@1.8.0 # buildkit

RUN /bin/sh -c curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py38_4.9.2-Linux-x86_64.sh && bash Miniconda3-py38_4.9.2-Linux-x86_64.sh -b -p /usr/local/miniconda && rm Miniconda3-py38_4.9.2-Linux-x86_64.sh # buildkit

ENV PATH=/usr/local/miniconda/bin:/usr/lib/ants:/usr/lib/fsl/5.0:/usr/lib/afni/bin:/opt/freesurfer/bin:/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin CPATH=/usr/local/miniconda/include: LANG=C.UTF-8 LC_ALL=C.UTF-8 PYTHONNOUSERSITE=1

RUN /bin/sh -c conda install -y python=3.8 pip=21.0 mkl=2021.2 mkl-service=2.3 numpy=1.18.1 scipy=1.6 scikit-learn=0.24 matplotlib=3.3 pandas=1.2 libxslt=1.1 traits=6.2 zstd=1.4; sync && chmod -R a+rX /usr/local/miniconda; sync && chmod +x /usr/local/miniconda/bin/*; sync && conda clean -y --all && sync && rm -rf ~/.conda ~/.cache/pip/*; sync # buildkit

ENV MKL_NUM_THREADS=1 OMP_NUM_THREADS=1

RUN /bin/sh -c useradd -m -s /bin/bash -G users xcp_d # buildkit

WORKDIR /home/xcp_d

ENV HOME=/home/xcp_d

RUN /bin/sh -c python -c "from matplotlib import font_manager" && sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" ) # buildkit

RUN /bin/sh -c pip install --no-cache-dir "templateflow ~= 0.6.1 " && python -c "from templateflow import api as tfapi; tfapi.get('MNI152NLin2009cAsym', resolution=2, suffix='T1w', desc=None); tfapi.get(template='MNI152NLin6Asym',resolution=2, suffix='T1w'); tfapi.get(template='fsLR',density='32k',suffix='sphere'); tfapi.get('MNI152NLin2009cAsym', resolution=1, desc='carpet',suffix='dseg'); tfapi.get(template='MNI152NLin2009cAsym',mode='image',suffix='xfm',extension='.h5'); tfapi.get(template='fsLR',density='32k',desc='vaavg', suffix='midthickness',extension='.gii'); tfapi.get('fsLR', density='32k'); " && find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && find $HOME/.cache/templateflow -type f -exec chmod go=u {} + # buildkit

RUN /bin/sh -c curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && dpkg -i pandoc-2.2.2.1-1-amd64.deb && rm pandoc-2.2.2.1-1-amd64.deb # buildkit

ARG VERSION=0.0.1

RUN |1 VERSION=0.0.1 /bin/sh -c find $HOME -type d -exec chmod go=u {} + && find $HOME -type f -exec chmod go=u {} + && rm -rf $HOME/.npm $HOME/.conda $HOME/.empty # buildkit

RUN |1 VERSION=0.0.1 /bin/sh -c ldconfig # buildkit

WORKDIR /tmp/

/bin/sh -c #(nop) COPY dir:2347b9350caf4fefed9947534cb6fef51e0a6ca74e9298e1315ceedb75011137 in /src/xcp_d

/bin/sh -c #(nop) ARG VERSION=0.0.1

|1 VERSION=0.1.0 /bin/sh -c echo "${VERSION}" > /src/xcp_d/xcp_d/VERSION && echo "include xcp_d/VERSION" >> /src/xcp_d/MANIFEST.in && pip install --no-cache-dir "/src/xcp_d[all]"

|1 VERSION=0.1.0 /bin/sh -c find $HOME -type d -exec chmod go=u {} + && find $HOME -type f -exec chmod go=u {} + && rm -rf $HOME/.npm $HOME/.conda $HOME/.empty

|1 VERSION=0.1.0 /bin/sh -c ldconfig

/bin/sh -c #(nop) WORKDIR /tmp/

/bin/sh -c #(nop) ENTRYPOINT ["/usr/local/miniconda/bin/xcp_d"]

/bin/sh -c #(nop) ARG BUILD_DATE

/bin/sh -c #(nop) ARG VCS_REF

/bin/sh -c #(nop) ARG VERSION

/bin/sh -c #(nop) LABEL org.label-schema.build-date=2022-07-15T01:27:56Z org.label-schema.name=xcp_d org.label-schema.description=xcp_d- postprocessing of fmriprep outputs org.label-schema.url=https://xcp-abcd.readthedocs.io/ org.label-schema.vcs-ref=ff3db26 org.label-schema.vcs-url=https://github.com/PennLINC/xcp_d org.label-schema.version=0.1.0 org.label-schema.schema-version=1.0