From 3774d08c76ac244e59802d44e2e730e02765a91d Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 26 Mar 2012 10:39:53 +0200
Subject: Misc bug fixes

---
 base-install.sh |  2 +-
 config.sh       | 19 ++++++-------------
 install         | 31 +++++++++++++------------------
 utils.sh        |  9 +++++++--
 4 files changed, 27 insertions(+), 34 deletions(-)

diff --git a/base-install.sh b/base-install.sh
index bbe8f4a..35b0515 100755
--- a/base-install.sh
+++ b/base-install.sh
@@ -34,7 +34,7 @@ fi
 touch "$OT_UI_CONF"
 
 # Pkgs
-packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev"
+packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev"
 
 echo
 echo "Base Packages:"
diff --git a/config.sh b/config.sh
index bd7f1ab..c951907 100755
--- a/config.sh
+++ b/config.sh
@@ -7,7 +7,7 @@
 # 1) Base setup
 OT_DIST="debian"       # Linux distribution    (debian)
 OT_INSTALL="local"     # Type                  (gem, local, server)
-OT_BRANCH="development"     # Maturity              (development -you need SSH key at Github-, master)
+OT_BRANCH="development"     # Maturity              (development -need SSH key at Github-, master)
 
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
@@ -16,28 +16,21 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
 # 3) What versions to install.
 RUBY_NUM_VER="1.9.3-p125"
 OB_NUM_VER="2.3.1"
-REDIS_NUM_VER="2.2.2"
 
 # 4) Server settings.
-NGINX_SERVERNAME="toxcreate3.in-silico.ch"
-WWW_DEST="$OT_PREFIX/www"
+SERVERNAME="toxcreate3.in-silico.ch"
 OHM_PORT="6381" # set to port (no colon)
 
 # Done.
 
 
 ### Nothing to gain from changes below this line.
-JAVA_CONF="$OT_PREFIX/.sh_java_ot"
-OB_CONF="$OT_PREFIX/.sh_OB_ot"
-R_CONF="$OT_PREFIX/.sh_R_ot"
+JAVA_CONF="$HOME/.opentox/sh_java"
+OB_CONF="$HOME/.opentox/sh_OB"
+R_CONF="$HOME/.opentox/sh_R"
+OT_UI_CONF="$HOME/.opentox/opentox-ui.sh"
 
 OB_VER="openbabel-$OB_NUM_VER"
-REDIS_VER="$REDIS_NUM_VER"
-
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-R_DEST="$OT_PREFIX/r-packages"
-REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
 
-REDIS_SERVER_CONF="$REDIS_DEST/redis.conf"
-OT_UI_CONF="$HOME/.opentox-ui.sh"
diff --git a/install b/install
index 1e4945b..9405f99 100755
--- a/install
+++ b/install
@@ -15,24 +15,19 @@ echo
 
 mkdir -p $OT_PREFIX/tmp/ >/dev/null 2>&1
 DATE=`date +_%Y%m%d_%H_%M`
-if [ -f "$HOME/.opentox-ui.sh" ]
-then
-  mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
-else
-  echo "$HOME/.opentox-ui.sh not found (nothing to backup)."
-fi
-if [ -d "$HOME/.opentox" ]
-then
-  mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE
-else
-  echo "$HOME/.opentox not found (nothing to backup)."
-fi
-if [ -d "$HOME/opentox-ruby" ]
-then
-  mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE
-else
-  echo "$HOME/opentox-ruby not found (nothing to backup)."
-fi 
+
+echo
+echo "Backups (if any)."
+echo
+backup_targets="$HOME/.opentox $HOME/opentox-ruby"
+for bt in $backup_targets; do
+  if [ -f $bt ]; then
+    mv -v --backup=numbered $bt $bt$DATE
+  elif [ -d $bt ]; then
+    mv -v --backup=numbered -T $bt $bt$DATE
+  fi
+done
+
 LOG="$OT_PREFIX/tmp/`basename $0`-log.txt"
 . "./utils.sh"
 echo
diff --git a/utils.sh b/utils.sh
index 0bc7801..04426d9 100755
--- a/utils.sh
+++ b/utils.sh
@@ -4,7 +4,12 @@ check_dest()
 {
   [ -d "$OT_PREFIX/tmp" ] || mkdir -p "$OT_PREFIX/tmp"
   if ! [ -d "$OT_PREFIX/tmp" ]; then
-    echo "Could not create target directory! Aborting..."
+    echo "Could not create OT_PREFIX directory! Aborting..."
+    exit 1
+  fi
+  [ -d "$HOME/.opentox" ] || mkdir -p "$HOME/.opentox"
+  if ! [ -d "$HOME/.opentox" ]; then
+    echo "Could not create .opentox directory! Aborting..."
     exit 1
   fi
 }
@@ -35,6 +40,6 @@ abs_path()
 }
 
 . "`pwd`/config.sh"
+check_dest
 touch "$OT_UI_CONF"
 . "$OT_UI_CONF" 2>/dev/null
-check_dest
-- 
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