neurodebian/neurodebian:latest

$ singularity pull shub://neurodebian/neurodebian:latest

Singularity Recipe

# Copyright (c) 2018-2019, Yaroslav O. Halchenko. All rights reserved. MIT license
#
# The purpose of the Singularity environment is to provide a relatively full
# suite of tools provided primarily by Debian/NeuroDebian for runnin various
# neuroimaging analyses.
#
# Notes:
#  - Due to  https://github.com/singularityware/singularity/issues/471
#    bootstrapping leads to non-usable/non-removable-without-reboot
#    image due to some rogue run away processes.
#    This line could help to kill them but should be used with caution
#    since could kill other unrelated processes
#
#      grep -l loop /proc/*/mountinfo | sed -e 's,/proc/\(.*\)/.*,\1,g' | while read pid; do sudo kill $pid; done
#
# Set size to be 12000 on singularity-hub
#
# Changelog
# ---------
# 10.20190801
#  - fresh versions of the packages
#  - base on recent Debian stable buster release (Debian 10)
#  - freezing using nd_freeze to the fixed day (2nd portion of the version)
#  - bids-validator 1.2.5
# 2.2
#  - fresh annex with patched git to avoid "Out of memory, getdelim failed" bug
#  - added some tools useful for debugging (gdb)
#  - additional mountpoints (/scratch)
#  - (note) pip is not installed on purpose, use the one within virtualenv(s)
# 2.x
#  - switch to stretch
#  - TODO make reproducible
#  - bids-validator from 0.22
#  - Added ants, convert3d
#
# TODOs
# -----
# - package bids-validator

BootStrap: debootstrap
OSVersion: buster
MirrorURL: http://http.debian.net/debian/
#MirrorURL: http://smaug.datalad.org:3142/debian/

# so if image is executed we just enter the environment
%runscript
    v=`python -c "import json; f='/.singularity.d/labels.json'; print(json.load(open(f)).get('SINGULARITY_IMAGE_VERSION', '0.0.unknown'))"`; \
      echo "Welcome to the NeuroDebian v $v (Debian stretch) environment"
    echo "Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI"
    /bin/bash

%setup
    set -eu
    export | grep SING
    echo "Setting up the environment"
    #apt-get update
    #apt-get -y install python 

    v=`git describe --tags --match sing-\* | sed -e 's,^sing-,,g'`; \
      python -c "import json, os; f='$SINGULARITY_ROOTFS/.singularity.d/labels.json'; j=json.load(open(f)) if os.path.exists(f) else {}; j['SINGULARITY_IMAGE_VERSION']='$v' or '0.0.unknown'; json.dump(j, open(f,'w'),indent=2)"
    chmod a+r "$SINGULARITY_ROOTFS/.singularity.d/labels.json"

%post
    echo "Configuring the environment"
    sed -i -e 's, main$, main contrib non-free,g' /etc/apt/sources.list
    # For build-dep
    # sed -i -e 's,^deb \(.*\),deb \1\ndeb-src \1,g' /etc/apt/sources.list
    apt-get update -q --no-allow-insecure-repositories
    apt-get -y install -q --no-install-recommends wget
    TMPBINDIR=/var/tmp
    mkdir -p $TMPBINDIR
    # eatmydata apt-get -y build-dep git
    wget --no-check-certificate  -O $TMPBINDIR/nd-configurerepo -nc \
      https://raw.githubusercontent.com/neurodebian/neurodebian/073c52d55f294e9535d683a630de9805e261b13f/tools/nd-configurerepo
    bash $TMPBINDIR/nd-configurerepo --mirror=default --install 
    chmod a+r -R /etc/apt
    apt-get update -q --no-allow-insecure-repositories
    apt-get install -y neurodebian-freeze
    nd_freeze 20190801
    # Needed for debian-security APT
    # echo 'Acquire::Check-Valid-Until "0";' > /etc/apt/apt.conf.d/10no--check-valid-until
    apt-get update --no-allow-insecure-repositories
 
    # Main installations
    apt-get -y install eatmydata 
    eatmydata apt-get -y install vim strace gdb time ncdu gnupg curl procps debian-goodies man-db
    bash -c 'eatmydata apt-get -y install git git-annex-standalone datalad python-{nipype,dipy} virtualenv dcm2niix python-dcmstack python-configparser python-funcsigs python-pytest connectome-workbench python-mvpa2 fsl-core fsl-atlases fsl-first-data mricron afni fsleyes heudiconv mrtrix3'
    # Electrophys packages
    eatmydata apt-get -y install python-pynwb python-biosig sigviewer
    # TODO: nilearn

    # for bids-validator
    curl -sL https://deb.nodesource.com/setup_6.x | bash - && \
       eatmydata apt-get install -y nodejs npm
    npm install -g bids-validator@1.2.5
    chmod a+rX -R /usr/lib/node_modules/ || :

    chmod a+rX -R /etc/apt/sources.list.d || :
    # cleaning /tmp that thoroughly might have side effects 
    # rm -rf /tmp/* /var/tmp/*
    apt-get clean
    rm -rf /tmp/npm-* /tmp/nd-config* /tmp/startup* /var/tmp/npm-* /var/lib/apt/lists/*

    # and wipe out apt lists since not to be used RW for further tuning
    # find /var/lib/apt/lists/ -type f -delete
    # /usr/bin/find /var/lib/apt/lists/ -type f -name \*Packages\* -o -name \*Contents\*
    # complicates later interrogation - thus disabled

    # Create some additional bind mount directories present on various compute boxes we have
    # access to, to ease deployment
    mkdir -p /afs /inbox /ihome /opt /data /backup /apps /srv /scratch /idata
    chmod a+rX /afs /inbox /ihome /opt /data /backup /apps /srv /scratch /idata

Collection

• Name: neurodebian/neurodebian
• License: None

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