Dockerfile_Micromamba

# Copied from: fMRIPrep Docker Container Image distribution
#
# MIT License
#
# Copyright (c) 2021 The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

FROM nvidia/cuda:11.2.2-devel-ubuntu18.04
ARG TAG_ANTS

RUN apt-get update && \
    apt-get install -y --no-install-recommends \
                    ca-certificates \
                    curl \
                    libblas-dev \
                    liblapack-dev \
                    build-essential \
                    libglu1-mesa-dev \
                    bzip2 \
                    libgomp1 \
                    wget

# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users qsirecon
WORKDIR /home/qsirecon
ENV HOME="/home/qsirecon"


WORKDIR /
RUN echo "2024.04.11"
RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba

ENV MAMBA_ROOT_PREFIX="/opt/conda" \
    MAMBA_NO_LOW_SPEED_LIMIT=1 \
    PIP_DEFAULT_TIMEOUT=100

COPY qsirecon_env.yml /tmp/env.yml

WORKDIR /tmp
RUN micromamba config set extract_threads 1
RUN micromamba create -vv -y -f /tmp/env.yml
ENV PATH=/opt/conda/envs/qsirecon/bin:$PATH
RUN micromamba clean -y -a

RUN \
  cd /tmp && \
  wget https://github.com/freesurfer/surfa/archive/refs/tags/v0.6.0.tar.gz && \
  tar xvfz v0.6.0.tar.gz && \
  cd surfa-0.6.0 && \
  python setup.py install && \
  cd .. && \
  rm -rf surfa-0.6.0 v0.6.0.tar.gz


RUN mkdir -p ${HOME}/.dipy \
    && python -c "import amico; amico.core.setup()"