install.sh

#!/bin/bash

# INSTALL SCRIPT

# assumes that getopts is installed
# possible options:
# -h (print usage)
# -q (quiet do not print progress)
# -d (desktop install, use full path in config)
# -j (print config in JSON format)
# -p <prefix> (path to install, default is ../)
# -c <file> (config file that has plugins, default plugins.json)

function readJSON {
  VALUE=`grep -m 1 "\"${2}\"" ${1} | sed 's/^ *//;s/.*: *//;s/,?//' | sed 's/,//'`
  if [ ! "$VALUE" ]; then
    echo false;
  else
    echo $VALUE;
  fi;
}

function useage(){
  echo ""
  echo "Usage: install.sh [-h] [-j] [-d] [-p <prefix>] [-c <config file>]"
  echo ""
  echo "  Will install the plugins specified in the config file located at path"
  echo "  When '-d' is not set, will print JBrowse config for the plugins installed to be included in"
  echo "  'jbrowse.conf' or 'jbrowse_conf.json' when -j is specified"
  echo ""
  echo "Options:"
  echo "-h         Print help menu"
  echo "-q         Quiet; don't print progress"
  echo "-j         Output JBrowse config in JSON format for 'jbrowse_conf.json'"
  echo "             Default outputs for 'jbrowse.conf'"
  echo "-d         Desktop install - always use full path in output config"
  echo "-p prefix  Install in this directory; default is '../' which"
  echo "             should be the JBrowse plugin folder"
  echo "-c config  JSON file specifying which plugins to install"
  echo "             default is 'plugins.json'"
}

function normalizePath {
  # remove /./ sequences
  local   path=${1//\/.\//\/}
  # Remove first dir/.. sequence.
  local   npath=$(echo $path | sed -e 's;[^/][^/]*/\.\./;;')

  # Remove remaining dir/.. sequence.
  while [[ $npath != $path ]]
  do
      path=$npath
      npath=$(echo $path | sed -e 's;[^/][^/]*/\.\./;;')
  done
  echo $path
}

function getConfPath {
  # $1 isDesktop? $2 currentPath $3 prefix
  desktop=$1
  curpath=$2
  prefix=$3
  isAbs=`echo $3 | grep -E '^\/' | wc -l`

  if [[ ${isAbs} -gt 0 ]]; then
  echo ${prefix}
  else
    if [[ $prefix == "../" && ${curpath} =~ plugins/(BhofmeiPlugins|bhofmei-jbplugins) && $desktop != "true" ]]; then
      echo "plugins/"
    else
      m=`normalizePath $curpath/$prefix`
      echo $m
    fi;
  fi;
}

function installPlugin {
  # $1 PREFIX $2 name $3 URL $4 isJson $5 configpath $quiet
  prefix=$1
  name=$2
  url=$3
  json=$4
  configpath=$5
  quiet=$6

  #echo "git clone ${quiet} ${url} ${prefix}${name}" >&2
  git clone ${quiet} ${url} ${prefix}${name}
  if [[ $json == "true" ]]; then
    echo "    \"${2}\" : { \"location\" : \"${configpath}${name}\" },"
  else
    echo -e "[plugins.${name}]\nlocation = ${configpath}${name}"
  fi
}

PREFIX="../"
JSON=false
DESKTOP=false
CONFIG="plugins.json"
QUIET=""

while getopts "hqjdp:c:" opt; do
  case $opt in
    j)
      JSON=true
      ;;
    d)
      DESKTOP=true
      ;;
    q)
      QUIET="-q"
      ;;
    p)
      PREFIX=$OPTARG
      ;;
    c)
      CONFIG=$OPTARG
      ;;
    h)
      useage
      exit 1
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      echo "Use -h for help"
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument" >&2
      echo "Use -h for help"
      exit 1
      ;;
  esac
done

curpath=`pwd`

# make sure path ends in /
PREFIX=`echo "${PREFIX}/" | sed 's/\/\//\//'`
EXPPATH=$PREFIX

## get the path to specify in the config file
EXPPATH=`getConfPath $DESKTOP $curpath $PREFIX`

BASE=https://github.com/bhofmei/
URLS=(jbplugin-hierarchicalcheckbox jbplugin-methylation jbplugin-motifdens jbplugin-seqview jbplugin-screenshot jbplugin-smallrna jbplugin-strandedplot jbplugin-trackscores jbplugin-wigglesvg jbplugin-yscale)
NAMES=(HierarchicalCheckboxPlugin MethylationPlugin MotifDensityPlugin SeqViewsPlugin ScreenShotPlugin SmallRNAPlugin StrandedPlotPlugin TrackScorePlugin WiggleSVGPlotPlugin YScaleMenuPlugin)

CONFTXT="" # output configuration text used for installation

for i in ${!NAMES[@]}; do
  name=${NAMES[i]}
  b=`readJSON ${CONFIG} ${name}`
  if [[ $b == "true" ]]; then
    u=${BASE}${URLS[i]}
    t=`installPlugin ${PREFIX} ${name} $u ${JSON} ${EXPPATH} ${QUIET}`
    CONFTXT=`echo -e "${CONFTXT}\n${t}"`
    #CONFTXT="${CONFTXT}${t}"
  fi;
done
# remove trailing comma if json format and add plugin section
if [[ $JSON == "true" ]]; then
  CONFTXT=${CONFTXT%?}
  CONFTXT=`echo -e "\"plugins\" : {${CONFTXT}\n}"`
fi;

# output results for config
  echo ""
  echo ""
  if [[ $JSON == "true" ]]; then
    echo "Include in 'jbrowse_conf.json' or 'trackList.json"
    echo ""
    echo "$CONFTXT"
    echo ""
    echo "Double check for correct JSON syntax"
  else
    echo "Include in [GENERAL] section of 'jbrowse.conf' or 'tracks.conf'"
    echo -e "$CONFTXT"
  fi
exit 0