Dockerfile.centos7

FROM centos:7.5.1804

MAINTAINER Tashrif Billah <tbillah@bwh.harvard.edu>

# set up user and working directory
ARG USER=pnlbwh
ENV USER="$USER"
ARG CWD=/root
WORKDIR $CWD
ENV PWD="$CWD"

# libraries and commands for FSL
RUN yum -y update \
    && yum -y install epel-release wget file bzip2 openblas-devel which \
    libmng libpng12 libSM gtk2 mesa-dri-drivers

# install FSL, -V 5.0.11, you are welcome to change it below
RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -O fslinstaller.py \
    && python fslinstaller.py -V 6.0.1 -d `pwd`/fsl-5.0.11-centos7 -p

# setup FSL environment
ENV FSLDIR="$PWD/fsl-5.0.11-centos7"
ENV PATH="$FSLDIR/bin/:$PATH" \
	FSLMULTIFILEQUIT=TRUE \
	FSLGECUDAQ=cuda.q \
	FSLTCLSH="$FSLDIR/bin/fsltclsh" \
	FSLWISH="$FSLDIR/bin/fslwish" \
	FSLOUTPUTTYPE=NIFTI_GZ


# apply patch
RUN $FSLDIR/fslpython/bin/conda install -y -n fslpython -c conda-forge deprecation==1.*