Dockerfile-freesurfer-dev

# This Dockerfile constructs a docker image, based on the vistalab/freesurfer
# docker image to execute recon-all as a Flywheel Gear.
#
# Example build:
#   docker build --no-cache --tag scitran/freesurfer-recon-all `pwd`
#
# Example usage:
#   docker run -v /path/to/your/subject:/input scitran/freesurfer-recon-all
#

FROM ubuntu:xenial
LABEL MAINTAINER="Michael Perry <lmperry@stanford.edu>"

# Install dependencies for FreeSurfer
RUN apt-get update && apt-get -y install \
        bc \
        tar \
        zip \
        wget \
        gawk \
        tcsh \
        python \
        libgomp1 \
        python2.7 \
        python-pip \
        perl-modules

# Download Freesurfer dev from MGH and untar to /opt
RUN wget -N -qO- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos6_x86_64-dev.tar.gz | tar -xz -C /opt && chown -R root:root /opt/freesurfer

# Make directory for flywheel spec (v0)
ENV FLYWHEEL /flywheel/v0
RUN mkdir -p ${FLYWHEEL}
WORKDIR ${FLYWHEEL}

# Run the run.sh script on entry.
ENTRYPOINT ["/flywheel/v0/run"]