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# 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
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