chrisvriend/ENIGMA_subthal:s3stretch

$ singularity pull shub://chrisvriend/ENIGMA_subthal:s3stretch

Singularity Recipe

# Your version: 0.6.0 Latest version: 0.6.0
# Generated by Neurodocker version 0.6.0
# Timestamp: 2020-03-03 09:25:37 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
#     https://github.com/kaczmarj/neurodocker

Bootstrap: docker
From: debian:stretch

%post
export ND_ENTRYPOINT="/neurodocker/mainscript.sh"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
    apt-utils \
    bzip2 \
    ca-certificates \
    curl \
    locales \
    time \
    unzip \
    procps
apt-get clean
rm -rf /var/lib/apt/lists/*
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
dpkg-reconfigure --frontend=noninteractive locales
update-locale LANG="en_US.UTF-8"
chmod 777 /opt && chmod a+s /opt
mkdir -p /neurodocker
if [ ! -f "$ND_ENTRYPOINT" ]; then
  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
  echo 'set -e' >> "$ND_ENTRYPOINT"
  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
fi
chmod -R 777 /neurodocker && chmod a+s /neurodocker


# download Python
export PATH="/opt/miniconda-latest/bin:$PATH"
echo "Downloading Miniconda installer ..."
conda_installer="/tmp/miniconda.sh"
curl -fsSL --retry 5 -o "$conda_installer" https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh
bash "$conda_installer" -b -p /opt/miniconda-latest
rm -f "$conda_installer"
conda update -y -q -nbase conda
conda config --system --prepend channels conda-forge
conda config --system --set auto_update_conda false
conda config --system --set show_channel_urls true
sync && conda clean -y --all && sync
conda create -y -q --name neuro
conda install -y -q --name neuro \
    "python=3.7" \
    "traits" \
    "numpy" \
    "pandas" \
    "seaborn=0.10.1" \
    "matplotlib"
sync && conda clean -y --all && sync
bash -c "source activate neuro
  pip install --no-cache-dir  \
      "ptitprince" \
      "nilearn" \
      "plotly""
rm -rf ~/.cache/pip/*
sync


apt-get update -qq
apt-get install -y -q --no-install-recommends \
    bc \
    libgomp1 \
    libxmu6 \
    libxt6 \
    perl \
    tcsh
apt-get clean
rm -rf /var/lib/apt/lists/*


echo "Downloading FreeSurfer ..."
mkdir -p /opt/freesurfer7
chmod -R 777 /opt/freesurfer7 && chmod a+s /opt/freesurfer7
curl -fsSL --retry 5 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-linux-centos6_x86_64-7.1.1.tar.gz \
| tar -xz -C /opt/freesurfer7 --strip-components 1 \
  --exclude='freesurfer/average/mult-comp-cor' \
  --exclude='freesurfer/average/BrainstemSS' \
  --exclude='freesurfer/average/Buckner_JNeurophysiol11_MNI152' \
  --exclude='freesurfer/average/Choi_JNeurophysiol12_MNI152' \
  --exclude='freesurfer/average/HippoSF' \
  --exclude='freesurfer/average/Yeo_Brainmap_MNI152' \
  --exclude='freesurfer/average/Yeo_JNeurophysiol11_MNI152' \
  --exclude='freesurfer/lib/cuda' \
  --exclude='freesurfer/lib/qt' \
  --exclude='freesurfer/subjects/V1_average' \
  --exclude='freesurfer/subjects/bert' \
  --exclude='freesurfer/subjects/cvs_avg35' \
  --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
  --exclude='freesurfer/subjects/fsaverage3' \
  --exclude='freesurfer/subjects/fsaverage4' \
  --exclude='freesurfer/subjects/fsaverage5' \
  --exclude='freesurfer/subjects/fsaverage6' \
  --exclude='freesurfer/subjects/fsaverage_sym' \
  --exclude='freesurfer/trctrain'
#sed -i '$isource "/opt/freesurfer7/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
# modify recon-all to only subsegment the thalamus
sed -i 's/set scrlist = (segmentHA_T1.sh segmentThalamicNuclei.sh segmentBS.sh)/set scrlist =  (segmentThalamicNuclei.sh)/g' /opt/freesurfer7/bin/recon-all

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    dc \
    file \
    libfontconfig1 \
    libfreetype6 \
    libgl1-mesa-dev \
    libgl1-mesa-dri \
    libglu1-mesa-dev \
    libice6 \
    libncurses5 \
    libxext6 \
    libxpm-dev \
    libxcursor1 \
    libxft2 \
    libxinerama1 \
    libxrandr2 \
    libxrender1 \
    sudo \
    wget
apt-get clean
rm -rf /var/lib/apt/lists/*

echo "Downloading FSL ..."
mkdir -p /opt/fsl-5.0.10
curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.10-centos6_64.tar.gz \
| tar -xz -C /opt/fsl-5.0.10 --strip-components 1
sed -i '$iecho Some packages in this container are non-free' $ND_ENTRYPOINT
sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT
sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT
sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT
echo "Installing FSL conda environment ..."
bash /opt/fsl-5.0.10/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.10


export TMPDIR="$(mktemp -d)"

echo "Downloading MATLAB Compiler Runtime ..."
curl -fsSL --retry 5 -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R2014b/deployment_files/R2014b/installers/glnxa64/MCR_R2014b_glnxa64_installer.zip
unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp"
"$TMPDIR/mcrtmp/install" -destinationFolder /opt/freesurfer7/MCRv84 -mode silent -agreeToLicense yes
mv -n /opt/freesurfer7/MCRv84/v84/* /opt/freesurfer7/MCRv84/
rm -rf "$TMPDIR"
unset TMPDIR
#####################
chmod u+x /neurodocker/mainscript.sh
chmod u+x /neurodocker/combine_subnuclei.sh
chmod u+x /neurodocker/extract_vols_plot.py
chmod u+x /neurodocker/create_webpage_thalsubs.sh

echo '{
\n  "pkg_manager": "apt",
\n  "instructions": [
\n    [
\n      "base",
\n      "Ubuntu:18.04"
\n    ],
\n    [
\n      "_header",
\n      {
\n        "version": "generic",
\n        "method": "custom"
\n      }
\n    ],
\n    [
\n      "freesurfer",
\n      {
\n        "version": "7.1.1"
\n      }
\n    ],
\n    [
\n      "fsl",
\n      {
\n        "version": "5.0.10"
\n      }
\n    ]
\n  ]
\n}' > /neurodocker/neurodocker_specs.json

%environment
export LANG="en_US.UTF-8"
export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/mainscript.sh"
export FREESURFER_HOME="/opt/freesurfer7"
export PATH="/opt/freesurfer7/bin:$PATH"
export FSLDIR="/opt/fsl-5.0.10"
export PATH="/opt/fsl-5.0.10/bin:$PATH"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"
export PATH="/opt/miniconda-latest/envs/neuro/lib/python3.7/site-packages:$PATH"
export PYTHONPATH="/opt//miniconda-latest/envs/neuro/lib/python3.7/site-packages:$PYTHONPATH"


%files
license.txt /opt/freesurfer7/
mainscript_v9.sh /neurodocker/mainscript.sh
combine_subnuclei_v3.sh /neurodocker/combine_subnuclei.sh
extract_vols_plot.py /neurodocker/extract_vols_plot.py
create_webpage_thalsubs.sh /neurodocker/create_webpage_thalsubs.sh
QA_thalseg_v2.sh /neurodocker/QA_thalseg.sh
thalseg2html.py /neurodocker/thalseg2html.py
REFERENCE_1subj_thalQC.html /neurodocker/
REFERENCE_avg_thalQC.html /neurodocker/


%runscript
/neurodocker/mainscript.sh "$@"

Collection

• Name: chrisvriend/ENIGMA_subthal
• License: Other

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