Merge pull request #19 from poldracklab/enh/docker-afni

ENH: Add AFNI to docker image

Author: oesteban

.circleci/config.yml

@@ -84,13 +84,13 @@ jobs:
             set -e
             if [[ "$success" = "0" ]]; then
                 echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:xenial-20191010
+                docker tag localhost:5000/ubuntu ubuntu:xenial-20200114
                 docker pull localhost:5000/nirodents
                 docker tag localhost:5000/nirodents nirodents:latest
             else
                 echo "Pulling from Docker Hub"
-                docker pull ubuntu:xenial-20191010
-                docker tag ubuntu:xenial-20191010 localhost:5000/ubuntu
+                docker pull ubuntu:xenial-20200114
+                docker tag ubuntu:xenial-20200114 localhost:5000/ubuntu
                 docker push localhost:5000/ubuntu
             fi
 

Dockerfile

@@ -1,22 +1,22 @@
 # Use Ubuntu 16.04 LTS
-FROM ubuntu:xenial-20191010
+FROM ubuntu:xenial-20200114
 
 # Pre-cache neurodebian key
 COPY docker/files/neurodebian.gpg /usr/local/etc/.neurodebian.gpg
 
 # Prepare environment
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    curl \
+                    autoconf \
+                    build-essential \
                     bzip2 \
                     ca-certificates \
-                    xvfb \
-                    cython3 \
-                    build-essential \
-                    autoconf \
+                    curl \
+                    git \
                     libtool \
+                    lsb-release \
                     pkg-config \
-                    git && \
+                    xvfb && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Installing ANTs 2.3.0 (NeuroDocker build)
@@ -26,6 +26,24 @@ RUN mkdir -p $ANTSPATH && \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH/bin:$PATH
 
+# Pre-cache neurodebian key
+COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
+# Installing Neurodebian packages (FSL, AFNI, git)
+RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
+    (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    afni=16.2.07~dfsg.1-5~nd16.04+1 && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV AFNI_MODELPATH="/usr/lib/afni/models" \
+    AFNI_IMSAVE_WARNINGS="NO" \
+    AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
+    AFNI_PLUGINPATH="/usr/lib/afni/plugins"
+ENV PATH="/usr/lib/afni/bin:$PATH"
+
 # Create a shared $HOME directory
 RUN useradd -m -s /bin/bash -G users nirodents
 WORKDIR /home/nirodents