TEST: Use FMRIPREP-based Docker file

effigies · effigies · commit 48e88b834e16 · 2017-08-31T10:34:24.000-07:00
diff --git a/Dockerfile b/Dockerfile
@@ -1,43 +1,93 @@
-# Copyright (c) 2016, The developers of the Stanford CRN
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright notice, this
-#   list of conditions and the following disclaimer.
-#
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the following disclaimer in the documentation
-#   and/or other materials provided with the distribution.
-#
-# * Neither the name of crn_base nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
-# This Dockerfile is to be built for testing purposes inside CircleCI,
-# not for distribution within Docker hub.
-# For that purpose, the Dockerfile is found in build/Dockerfile.
+# Use Ubuntu 16.04 LTS
+FROM ubuntu:xenial-20161213
 
-FROM poldracklab/neuroimaging-core:freesurfer-0.0.2
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
 
-# Install cwebp
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    curl \
+                    bzip2 \
+                    ca-certificates \
+                    xvfb \
+                    cython3 \
+                    build-essential \
+                    autoconf \
+                    libtool \
+                    pkg-config && \
+    curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /root/.neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
+    apt-get update
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+    --exclude='freesurfer/trctrain' \
+    --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/V1_average' \
+    --exclude='freesurfer/average/mult-comp-cor' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt'
+
+ENV FSL_DIR=/usr/share/fsl/5.0 \
+    OS=Linux \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA= \
+    FSF_OUTPUT_FORMAT=nii.gz \
+    FREESURFER_HOME=/opt/freesurfer
+ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
+    FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
+    MNI_DIR=$FREESURFER_HOME/mni \
+    LOCAL_DIR=$FREESURFER_HOME/local \
+    FSFAST_HOME=$FREESURFER_HOME/fsfast \
+    MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
+    MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
+    MNI_DATAPATH=$FREESURFER_HOME/mni/data \
+    FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
+ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
+    PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
+RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
+
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    fsl-core=5.0.9-4~nd16.04+1 \
+                    fsl-mni152-templates=5.0.7-2 \
+                    afni=16.2.07~dfsg.1-5~nd16.04+1
+
+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:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    AFNI_MODELPATH=/usr/lib/afni/models \
+    AFNI_IMSAVE_WARNINGS=NO \
+    AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
+    AFNI_PLUGINPATH=/usr/lib/afni/plugins
+ENV PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
+
+# Installing ANTs 2.2.0 (NeuroDocker build)
+ENV ANTSPATH=/usr/lib/ants
+RUN mkdir -p $ANTSPATH && \
+    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    | tar -xzC $ANTSPATH --strip-components 1
+ENV PATH=$ANTSPATH:$PATH
+
+# Installing WEBP tools
 RUN curl -sSLO "http://downloads.webmproject.org/releases/webp/libwebp-0.5.2-linux-x86-64.tar.gz" && \
   tar -xf libwebp-0.5.2-linux-x86-64.tar.gz && cd libwebp-0.5.2-linux-x86-64/bin && \
   mv cwebp /usr/local/bin/ && rm -rf libwebp-0.5.2-linux-x86-64
 
-# Install nodejs -> svgo
+# Installing SVGO
 RUN curl -sL https://deb.nodesource.com/setup_7.x | bash -
 RUN apt-get install -y nodejs
 RUN npm install -g svgo
@@ -73,4 +123,4 @@ RUN cd niworkflows && \
     python -c 'from niworkflows.data.getters import get_mni_template_ras; get_mni_template_ras()' && \
     python -c 'from niworkflows.data.getters import get_ds003_downsampled; get_ds003_downsampled()' && \
     python -c 'from niworkflows.data.getters import get_ants_oasis_template_ras; get_ants_oasis_template_ras()' && \
-    python -c 'from niworkflows.data.getters import get_mni_icbm152_nlin_asym_09c; get_mni_icbm152_nlin_asym_09c()'
+    python -c 'from niworkflows.data.getters import get_mni_icbm152_nlin_asym_09c; get_mni_icbm152_nlin_asym_09c()'
diff --git a/circle.yml b/circle.yml
@@ -18,12 +18,9 @@ dependencies:
     - git submodule init && (git submodule update || true)
     - git submodule sync && git -C nipype fetch origin && git submodule update
   override:
-    - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi :
-        timeout: 6000
+    - docker pull poldracklab/fmriprep:latest || true
     - docker build --rm=false -t niworkflows:py3 .
     - docker build --rm=false -t niworkflows:py2 --build-arg PYTHON_MAJOR=2 .
-    - docker save poldracklab/neuroimaging-core:freesurfer-0.0.2 niworkflows:py3 niworkflows:py2 > ~/docker/image.tar :
-        timeout: 6000
 test:
   override:
     - bash .circle/pytests.sh :
diff --git a/docker/files/neurodebian.gpg b/docker/files/neurodebian.gpg
@@ -0,0 +1,71 @@
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