rmarkello/antslct:latest

$ singularity pull shub://rmarkello/antslct:latest

Singularity Recipe

# Generated by Neurodocker version 0.5.0
# Timestamp: 2019-08-27 16:51:34 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: ubuntu:18.04

%post
export ND_ENTRYPOINT="/neurodocker/startup.sh"
apt-get update -qq
apt-get install -y -q --no-install-recommends \
    apt-utils \
    bzip2 \
    ca-certificates \
    curl \
    locales \
    unzip
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

apt-get update -qq
apt-get install -y -q --no-install-recommends \
    bc \
    wget
apt-get clean
rm -rf /var/lib/apt/lists/*

mkdir -p /data /output

curl -sSL --retry 5 https://ndownloader.figshare.com/files/10454170?private_link=5d9349701c771e8d8d46 | tar zx -C /opt

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.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash "$conda_installer" -b -p /opt/miniconda-latest
rm -f "$conda_installer"
conda update -yq -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 --all && sync
conda env create -q --name antslct --file /opt/environment.yml
rm -rf ~/.cache/pip/*
sed -i '$isource activate antslct' $ND_ENTRYPOINT


echo "Downloading ANTs ..."
mkdir -p /opt/ants/bin
curl -fsSL --retry 5 https://dl.dropbox.com/s/1xfhydsf4t4qoxg/ants-Linux-centos6_x86_64-v2.3.1.tar.gz \
| tar -xz -C /opt/ants/bin --strip-components 1

if [ ! -f /opt/entrypoint.sh ]; then
      echo '#!/bin/bash
/opt/antslct.sh "${@}"' >> /opt/entrypoint.sh;
      chmod 777 /opt/entrypoint.sh;
      fi

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      "install",
\n      [
\n        "bc",
\n        "wget"
\n      ]
\n    ],
\n    [
\n      "run",
\n      "mkdir -p /data /output"
\n    ],
\n    [
\n      "run",
\n      "curl -sSL --retry 5 https://ndownloader.figshare.com/files/10454170?private_link=5d9349701c771e8d8d46 | tar zx -C /opt"
\n    ],
\n    [
\n      "copy",
\n      [
\n        "environment.yml",
\n        "/opt/environment.yml"
\n      ]
\n    ],
\n    [
\n      "miniconda",
\n      {
\n        "create_env": "antslct",
\n        "yaml_file": "/opt/environment.yml",
\n        "activate": true
\n      }
\n    ],
\n    [
\n      "ants",
\n      {
\n        "version": "2.3.1",
\n        "install_path": "/opt/ants/bin"
\n      }
\n    ],
\n    [
\n      "copy",
\n      [
\n        "code/antslct.sh",
\n        "/opt"
\n      ]
\n    ],
\n    [
\n      "copy",
\n      [
\n        "code/report.py",
\n        "/opt"
\n      ]
\n    ],
\n    [
\n      "copy",
\n      [
\n        "code/report.tpl",
\n        "/opt"
\n      ]
\n    ],
\n    [
\n      "run",
\n      "if [ ! -f /opt/entrypoint.sh ]; then\\n      echo '"'"'#!/bin/bash\\n/opt/antslct.sh \"${@}\"'"'"' >> /opt/entrypoint.sh;\\n      chmod 777 /opt/entrypoint.sh;\\n      fi"
\n    ],
\n    [
\n      "entrypoint",
\n      "/opt/entrypoint.sh \"${@}\""
\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/startup.sh"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"
export ANTSPATH="/opt/ants/bin"
export PATH="/opt/ants/bin:$PATH"

%files
environment.yml /opt/environment.yml
code/antslct.sh /opt
code/report.py /opt
code/report.tpl /opt

%runscript
/opt/entrypoint.sh "${@}"

Collection

• Name: rmarkello/antslct
• License: BSD 3-Clause “New” or “Revised” License

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.