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#!/bin/sh
# Installs Opentox Webservice.
# Author: Christoph Helma, Andreas Maunz.
SELF=$(basename $0 -install)
[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1
SILENT=false
if [ -n "$1" ]
then
if [ "$1" = "silent" ]
then
SILENT=true
fi
fi
if [ $SILENT = false ]; then
echo
echo "Welcome to service installation (<Return> to continue)."
read delete_me
fi
# check wd is root of service
DIR=`pwd`
if echo $DIR | grep "$SELF/bin" >/dev/null 2>&1 ; then cd ..; fi
# # # Boot the script
# load base config, helper funs, environment
OT_CONFIG_DIR="$HOME/.opentox"
! [ -f "$OT_CONFIG_DIR/config/install/config.sh" ] && echo "config.sh not found." 1>&2 && exit 1 || . $OT_CONFIG_DIR/config/install/config.sh
! [ -f "$OT_PREFIX/install/utils.sh" ] && echo "utils.sh not found." 1>&2 && exit 1 || . $OT_PREFIX/install/utils.sh
[ -f $OT_CONFIG_DIR/opentox-ui.sh ] && . $OT_CONFIG_DIR/opentox-ui.sh # should have been done by user already
RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER"
# # # Install
check_utils "rbenv find R javac"
check_log $SELF
if [ "$OT_BRANCH" = "development" ]; then
cmd="test -d $OT_PREFIX/opentox-server" && run_cmd "$cmd" "Opentox-server"
cmd="test -d $OT_PREFIX/opentox-client" && run_cmd "$cmd" "Opentox-client"
fi
# log directory for this service
[ -d $OT_CONFIG_DIR/config/$SELF ] || cmd="mkdir -p $OT_CONFIG_DIR/config/$SELF" && run_cmd "$cmd" "Config directory"
echo
cd $DIR/../java
cmd="$JAVAC -classpath classes:* *.java 2>&1" && run_cmd "$cmd" "Compile Algorithm java classes"
cd $DIR/..
sed -i "1irequire 'openbabel'" application.rb
# Adjust ruby version here!
RUBY_NUM_VER="2.0.0-p481"
# ruby
install_ruby
# fminer
( [ -n "`$FIND libfminer/ -name bbrc.so 2>/dev/null`" ] && [ -n "`$FIND libfminer/ -name last.so 2>/dev/null`" ] ) || . ./bin/fminer-install
# R
R_DONE=false
mkdir "$R_DEST" >/dev/null 2>&1
if [ ! -d "$R_DEST" ]; then
echo "Install directory '$R_DEST' is not available! Aborting..."
exit 1
else
if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail
R_DONE=true
else
mkdir "$R_DEST" >/dev/null 2>&1
fi
fi
if ! $R_DONE; then
export R_LIBS="$R_DEST" # To install non-global
cmd="$R CMD BATCH bin/packs.R" && run_cmd "$cmd" "R packages"
fi
# self
echo
install_with_bundler
# config
[ -f $OT_CONFIG_DIR/config/$SELF.rb ] || touch $OT_CONFIG_DIR/config/$SELF.rb
if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi
if ! cat "$OT_CONFIG_DIR/config/$SELF.rb" | grep "aa">/dev/null 2>&1; then echo '$aa = { :uri => nil }' >> $OT_CONFIG_DIR/config/$SELF.rb; fi
if ! cat "$OT_DEFAULT_CONF" | grep "$SELF">/dev/null 2>&1; then echo '$algorithm = { :uri => "http://localhost:8081/algorithm" }' >> $OT_DEFAULT_CONF; fi
if [ ! -f $R_CONF ]; then
echo "if echo \"\$R_LIBS\" | grep -v \"$R_DEST\">/dev/null 2>&1; then export R_LIBS=\"$R_DEST\"; fi" >> "$R_CONF"
echo "if ! [ -d \"$R_DEST\" ]; then echo \"\$0: '$R_DEST' is not a directory!\"; fi" >> "$R_CONF"
echo "R package destination stored in '$R_CONF'."
if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
echo ". \"$R_CONF\"" >> $OT_UI_CONF
fi
fi
if [ $SILENT = false ]; then
notify
fi
# return to wd
cd "$DIR"
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