MNT: Add dockerfile to build runtime image

.docker/bip-dev/README.md

+This docker image is used for running unit tests on the BIP code base. It can
+be built via Gitlab CI / CD by running the `build-dev-docker-image` job.
+
+At the moment the image is published to
+https://hub.docker.com/u/pauldmccarthy/bip-dev/.
\ No newline at end of file

.docker/create_dev_env.sh → .docker/bip-dev/create_dev_env.sh

@@ -31,7 +31,7 @@ echo "  conda-forge"                                                   >> ${envd
 
 source activate ${envdir}
 pip install dmri-amico
-pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/pipe-tree.git
+pip install git+https://git.fmrib.ox.ac.uk/fsl/pipe-tree.git
 
 conda remove -p ${envdir} c-compiler cxx-compiler
 conda clean -y -all

.docker/bip-image/Dockerfile

+FROM nvidia/cuda:11.0.3-base-centos7 as base
+
+ENV NVARCH                     x86_64
+ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
+ENV NVIDIA_REQUIRE_CUDA        cuda>=11.0 brand=tesla,driver>=418,driver<419
+ENV NVIDIA_VISIBLE_DEVICES     all
+ENV NV_CUDA_CUDART_VERSION     11.0.221-1
+
+COPY /build_image.sh /build_image.sh
+RUN /bin/bash /build_image.sh && rm /build_image.sh

.docker/bip-image/README.md

+BIP Docker image
+----------------
+
+
+The `Dockerfile` can be used to create a Docker image which contains BIP and
+all of its dependencies. The image contains a full BIP runtime environment,
+including FSL, FreeSurfer and Connectome Workbench. Be warned that the image
+is quite large, on the order of 15GB.
+
+
+1. Clone the BIP repository and change into the image directory:
+   ```
+   git clone https://git.fmrib.ox.ac.uk/fsl/bip.git
+   cd bip/.docker/bip-image
+   ```
+
+2. Build the image:
+
+   ```
+   docker build . -t bip &> build_log.txt
+   ```
+
+3. If the image was built on a different machine than the one it is to be run
+   on, save it to a `.tar.gz` archive:
+   ```
+   docker save bip | gzip -c > bip.tar.gz
+   ```
+
+   Then download the archive to the target machine, and load it:
+
+   ```
+   docker load < bip.tar.gz
+   ```
+
+4. Start a container from the image. Replace `<freesurfer-license>` with the
+   full path to your FreeSurfer license file.
+
+   ```
+   docker run -it                                              \
+     -v <freesurfer-license>:/usr/local/freesurfer/license.txt \
+     bip /bin/bash
+   ```

.docker/bip-image/build_image.sh

+#!/usr/bin/env bash
+
+set -e
+
+SHELL_PROFILE=/root/.bashrc
+
+export TAR_OPTIONS=--no-same-owner
+export WGET_OPTIONS=--no-check-certificate
+
+# OS / build dependencies
+yum install -y epel-release
+yum install -y openssh-clients git nano wget curl unzip python3 parallel
+
+# FSL
+FSL_URL=https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
+wget ${WGET_OPTIONS} ${FSL_URL} -O fslinstaller.py
+python /tmp/fslinstaller.py -V 6.0.7.6 -d /usr/local/fsl
+echo -e '\nexport FSLDIR=/usr/local/fsl/\n'       >> ${SHELL_PROFILE}
+echo -e '\nsource ${FSLDIR}/etc/fslconf/fsl.sh\n' >> ${SHELL_PROFILE}
+rm fslinstaller.py
+
+# BIP
+/usr/local/fsl/bin/mamba install -y -n base fsl-bip
+
+# ROBEX
+ROBEX_URL=https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//\?i_agree\=1\&download_now\=1
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${ROBEX_URL} -O ROBEX.tar.gz
+tar xf ROBEX.tar.gz && rm ROBEX.tar.gz
+echo -e '\nexport PATH=/usr/local/ROBEX:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Brainsuite
+BRAINSUITE_URL=http://brainsuite.org/data/BIDS/bse15c.biobank.tgz
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${BRAINSUITE_URL} -O brainsuite.tgz
+tar -xf brainsuite.tgz && rm brainsuite.tgz
+chmod -R ugo+rx BrainSuite15c
+echo -e '\nexport PATH=/usr/local/BrainSuite15c/bin:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Workbench
+WORKBENCH_URL=https://humanconnectome.org/storage/app/media/workbench/workbench-rh_linux64-v1.5.0.zip
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${WORKBENCH_URL} -O workbench.zip
+unzip workbench.zip && rm workbench.zip
+echo -e '\nexport PATH=/usr/local/workbench/bin_rh_linux64:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Freesurfer
+FREESURFER_URL=https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${FREESURFER_URL} -O freesurfer.tgz
+tar xf freesurfer.tgz && rm freesurfer.tgz
+echo -e '\nexport FREESURFER_HOME=/usr/local/freesurfer\n' >> ${SHELL_PROFILE}
+echo -e '\nsource ${FREESURFER_HOME}/SetUpFreeSurfer.sh\n' >> ${SHELL_PROFILE}
+popd
+
+# Clean up
+/usr/local/fsl/bin/mamba clean --all --yes --force-pkgs-dirs
+rm -rf /tmp/*
+rm -rf ${HOME}/.cache/
+yum clean all
+rm -rf /var/cache/yum/*