pennlinc
    xcp_d
    04.0
Namespace
pennlinc
Image / Tag
xcp_d:04.0
Content Digest
sha256:fe39ee765dea71b64ff2b7fc5c14e430e4087950f0b154815b02646bd5666a03
Details
Created

2023-06-12 13:50:29 UTC

Size

6.31 GB

Content Digest
Labels
  • org.label-schema.build-date
    2023-06-12T13:46:30Z
  • org.label-schema.description
    xcp_d- postprocessing of fmriprep outputs
  • org.label-schema.name
    xcp_d
  • org.label-schema.schema-version
    1.0
  • org.label-schema.url
    https://xcp-d.readthedocs.io/
  • org.label-schema.vcs-ref
    bb3e716
  • org.label-schema.vcs-url
    https://github.com/PennLINC/xcp_d
  • org.label-schema.version
    04.0
Environment
AFNI_IMSAVE_WARNINGS

NO

AFNI_MODELPATH

/usr/lib/afni/models

AFNI_PLUGINPATH

/usr/lib/afni/plugins

AFNI_TTATLAS_DATASET

/usr/share/afni/atlases

ANTSPATH

/usr/lib/ants

C3DPATH

/opt/c3d/bin

CPATH

/usr/local/miniconda/include:

FIX_VERTEX_AREA

FREESURFER_HOME

/opt/freesurfer

FSF_OUTPUT_FORMAT

nii.gz

FSLDIR

/opt/fsl

FSLGECUDAQ

cuda.q

FSLLOCKDIR

FSLMACHINELIST

FSLMULTIFILEQUIT

TRUE

FSLOUTPUTTYPE

NIFTI_GZ

FSLREMOTECALL

FSL_DEPS

libquadmath0;libnewimage.so;libmiscmaths.so

FUNCTIONALS_DIR

/opt/freesurfer/sessions

HOME

/home/xcp_d

LANG

C.UTF-8

LC_ALL

C.UTF-8

LD_LIBRARY_PATH

/opt/fsl/lib:

LOCAL_DIR

/opt/freesurfer/local

MINC_BIN_DIR

/opt/freesurfer/mni/bin

MINC_LIB_DIR

/opt/freesurfer/mni/lib

MKL_NUM_THREADS

1

MNI_DATAPATH

/opt/freesurfer/mni/data

MNI_DIR

/opt/freesurfer/mni

MNI_PERL5LIB

/opt/freesurfer/mni/lib/perl5/5.8.5

OMP_NUM_THREADS

1

OS

Linux

PATH

/usr/lib/ants:/usr/lib/afni/bin:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/lib:/opt/fsl/bin:/usr/local/miniconda/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

PERL5LIB

/opt/freesurfer/mni/lib/perl5/5.8.5

PYTHONNOUSERSITE

1

SUBJECTS_DIR

/opt/freesurfer/subjects

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History
2022-06-06 22:21:04 UTC

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

2022-06-06 22:21:05 UTC

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

2023-02-18 13:17:12 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:18:36 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c apt-get update && apt-get install -y --no-install-recommends apt-utils autoconf build-essential bzip2 ca-certificates curl dc git graphviz libtool locales pandoc pandoc-citeproc pkg-config unzip wget xvfb && 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

2023-02-18 13:18:39 UTC (buildkit.dockerfile.v0)

ENV OS=Linux FIX_VERTEX_AREA=

2023-02-18 13:18:39 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:18:39 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:18:53 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:19:15 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:19:15 UTC (buildkit.dockerfile.v0)

ENV PATH=/usr/local/miniconda/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

2023-02-18 13:20:42 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c conda install -y python=3.8 libxslt=1.1 matplotlib=3.3 mkl=2021.2 mkl-service=2.3 numpy=1.18.1 pandas=1.2 scikit-learn=0.24 scipy=1.6 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 && conda clean -tipsy; sync && rm -rf ~/.conda ~/.cache/pip/*; sync # buildkit

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends 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

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/slicer /opt/fsl/lib/slicer # buildkit

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/slicesdir /opt/fsl/lib/slicesdir # buildkit

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/pngappend /opt/fsl/lib/pngappend # buildkit

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/remove_ext /opt/fsl/lib/remove_ext # buildkit

2023-02-18 13:21:10 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-slicer /opt/fsl/bin/fsl-5.0-slicer # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-slicesdir /opt/fsl/bin/fsl5.0-slicesdir # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-pngappend /opt/fsl/bin/fsl5.0-pngappend # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-remove_ext /opt/fsl/bin/fsl5.0-remove_ext # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/slicer /opt/fsl/bin/slicer # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/slicesdir /opt/fsl/bin/slicesdir # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/pngappend /opt/fsl/bin/pngappend # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/remove_ext /opt/fsl/bin/remove_ext # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libnewimage.so /opt/fsl/lib/libnewimage.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libmiscmaths.so /opt/fsl/lib/libmiscmaths.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libmiscpic.so /opt/fsl/lib/libmiscpic.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libfslio.so /opt/fsl/lib/libfslio.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libutils.so /opt/fsl/lib/libutils.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libprob.so /opt/fsl/lib/libprob.so # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/libnewmat.so.10.0.0 /opt/fsl/lib/libnewmat.so.10 # buildkit

2023-02-18 13:21:11 UTC (buildkit.dockerfile.v0)

ENV FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE FSLLOCKDIR= FSLMACHINELIST= FSLREMOTECALL= FSLGECUDAQ=cuda.q LD_LIBRARY_PATH=/opt/fsl/lib: PATH=/opt/fsl/lib:/opt/fsl/bin:/usr/local/miniconda/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin FSL_DEPS=libquadmath0;libnewimage.so;libmiscmaths.so

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

ENV AFNI_MODELPATH=/usr/lib/afni/models AFNI_IMSAVE_WARNINGS=NO AFNI_TTATLAS_DATASET=/usr/share/afni/atlases AFNI_PLUGINPATH=/usr/lib/afni/plugins PATH=/usr/lib/afni/bin:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/lib:/opt/fsl/bin:/usr/local/miniconda/bin:/opt/c3d/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

2023-02-18 13:22:44 UTC (buildkit.dockerfile.v0)

ENV ANTSPATH=/usr/lib/ants

2023-02-18 13:23:00 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:00 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:06 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:08 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:10 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:35 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:35 UTC (buildkit.dockerfile.v0)

ENV MKL_NUM_THREADS=1 OMP_NUM_THREADS=1

2023-02-18 13:23:36 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:36 UTC (buildkit.dockerfile.v0)

WORKDIR /home/xcp_d

2023-02-18 13:23:36 UTC (buildkit.dockerfile.v0)

ENV HOME=/home/xcp_d

2023-02-18 13:23:38 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c pip install --no-cache-dir --upgrade pip # buildkit

2023-02-18 13:23:39 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:56 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c pip install --no-cache-dir "templateflow ~= 0.8.1 " && 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

2023-02-18 13:23:59 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:23:59 UTC (buildkit.dockerfile.v0)

ARG VERSION=0.0.1

2023-02-18 13:24:01 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:24:01 UTC (buildkit.dockerfile.v0)

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

2023-02-18 13:24:01 UTC (buildkit.dockerfile.v0)

WORKDIR /tmp/

2023-06-12 13:49:24 UTC

/bin/sh -c #(nop) COPY dir:966405a3cd6809826db7f7ab95b132c3ecaa56b0ef85cd05f3ddf80ad7464455 in /src/xcp_d

2023-06-12 13:49:25 UTC

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

2023-06-12 13:50:22 UTC

|1 VERSION=04.0 /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]"

2023-06-12 13:50:27 UTC

|1 VERSION=04.0 /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

2023-06-12 13:50:28 UTC

|1 VERSION=04.0 /bin/sh -c ldconfig

2023-06-12 13:50:28 UTC

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

2023-06-12 13:50:28 UTC

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

2023-06-12 13:50:28 UTC

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

2023-06-12 13:50:28 UTC

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

2023-06-12 13:50:28 UTC

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

2023-06-12 13:50:29 UTC

/bin/sh -c #(nop) LABEL org.label-schema.build-date=2023-06-12T13:46:30Z org.label-schema.name=xcp_d org.label-schema.description=xcp_d- postprocessing of fmriprep outputs org.label-schema.url=https://xcp-d.readthedocs.io/ org.label-schema.vcs-ref=bb3e716 org.label-schema.vcs-url=https://github.com/PennLINC/xcp_d org.label-schema.version=04.0 org.label-schema.schema-version=1.0

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For example when you have latest and v1.2.3 both pointing to the same image
the deletion of latest will also permanently remove v1.2.3.

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