Simple_Prep_docker

#!/bin/bash
#emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: t -*- 
#ex: set sts=4 ts=4 sw=4 noet:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
#   See COPYING file distributed along with the simple_workflow package for the
#   copyright and license terms.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# Helper to generate a Docker instance given release and snapshots date specification
# and run simple_workflow analysis
#
set -e
export PS4=+
#set -x
set -u

# a little helper since sed on OSX does not have sed -i
# for in-place modifications.  Note that filename here comes first
# just to ease scripting
sed-i () {
  filename=$1
  tfilename=$(mktemp -t sed_replace.XXXXXXXXX)
  shift
  sed "$@" "$filename" >| "$tfilename"
  mv "$tfilename" "$filename"
}

DL_DIST=${1:-jessie}
DL_DATE=${2:-}

cd `dirname $0`
dockerfile=./Simple_Prep_docker-Dockerfile
# echo "D: $DL_APT"
# Some substitutes aren't used but left for possibly later use
sed -e "s,DL_DIST,$DL_DIST,g" \
    -e "s,DL_USER,$USER,g" \
    -e "s,DL_UID,`id -u`,g" \
    -e "s,DL_GID,`id -g`,g" \
    -e "s,DL_GIT_USER_EMAIL,`git config --get user.email`,g" \
    -e "s,DL_GIT_USER_NAME,`git config --get user.name`,g" \
    $dockerfile.in >| $dockerfile

if [ ! -z "$DL_DATE" ]; then
{
    # replace with snapshots.  Since ran inside the container, sed -i should be ok
    echo "sed -i -e 's,http://neuro.debian.net/debian/* ,http://snapshot-neuro.debian.net:5002/archive/neurodebian/$DL_DATE/ ,g' etc/apt/sources.list.d/neurodebian.sources.list"
    # for now we need to knock to expose snapshots repository
    echo "curl -s http://neuro.debian.net/_files/knock-snapshots;"
    # TODO: figure out and add snapshot for DL_DIST itself if available and force possible downgrade somehow
    echo "eatmydata apt-get update; eatmydata apt-get dist-upgrade -y;"
} | while read aptline; do
    # on OSX cannot use \n to get a newline in sed, so doing POSIX way, although also escaping trailing \
    # so it is in effect within sed-i call
    sed-i "$dockerfile" -e "s|\(\(.*\)DL_APT\(.*\)\)|\2$aptline\3\\
\1|g"
    :
done
fi

# for debugging
# cat $dockerfile
sed-i "$dockerfile" -e '/DL_APT/d'

tag_=simple_prep_${USER}_${DL_DIST}_${DL_DATE}
tag=repronim:${tag_}
echo "I: tag $tag"
if [ $(command -v docker) ]; then
    docker build -t $tag -f $dockerfile .
else
    echo "Could not find docker. Please install and rerun script"
    exit 1
fi