From 1c63985d4100ca7a7e90b03f8e6b9412ec71d20b Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 31 Oct 2011 10:52:22 +0100
Subject: Fixing symlink creation: restored '/' at end of target path

---
 README | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README b/README
index 375d22f..79c6569 100644
--- a/README
+++ b/README
@@ -67,7 +67,7 @@ otupdate() {
     echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
     rm -rf "$LINK_DIR~"
     mv "$LINK_DIR" "$LINK_DIR~"
-    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-4}`
+    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}`
   fi
   echo "Please execute 'otstart' to restart."
   cd "$START_DIR"
-- 
cgit v1.2.3


From a6c10ced1118e9b6513a1a24456c5bf35dda7b4b Mon Sep 17 00:00:00 2001
From: David Vorgrimmler <vorgrimmlerdavid@gmx.de>
Date: Fri, 11 Nov 2011 11:05:06 +0100
Subject: Added tmp folder to .opentox

---
 opentox-ruby.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 5f8cc65..70d502b 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -66,6 +66,7 @@ fi
 
 mkdir -p "$HOME/.opentox/config" >>$LOG 2>&1
 mkdir -p "$HOME/.opentox/log" >>$LOG 2>&1
+mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1
 
 $GIT checkout production.yaml      >>$LOG 2>&1
 $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
-- 
cgit v1.2.3


From c81acb5265a6a281d2757710f36e2e6e2e48986e Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 15 Nov 2011 14:04:05 +0100
Subject: Added support for PORT

---
 aa-local.yaml   | 30 +++++++++++++++---------------
 aa-server.yaml  | 30 +++++++++++++++---------------
 config.sh       |  1 +
 nginx.conf      | 14 +++++++-------
 nginx.sh        |  5 +++++
 opentox-ruby.sh |  4 ++--
 production.yaml | 14 +++++++-------
 7 files changed, 52 insertions(+), 46 deletions(-)

diff --git a/aa-local.yaml b/aa-local.yaml
index 260c72e..5ca2b72 100644
--- a/aa-local.yaml
+++ b/aa-local.yaml
@@ -15,25 +15,25 @@
 # Exceptions:
   :free_uris: #request-method for uri not controlled by A&A
     ? - :GET
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
-      - "http://SERVERNAME/model"
-      - "http://SERVERNAME/dataset"
-      - "http://SERVERNAME/validation"
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/resources/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
+      - "http://SERVERNAMEPORT/model"
+      - "http://SERVERNAMEPORT/dataset"
+      - "http://SERVERNAMEPORT/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/resources/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/compound/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/compound/
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
-      - "http://SERVERNAME/dataset"
-      - "http://SERVERNAME/model"
-      - "http://SERVERNAME/validation"
-      - !ruby/regexp /http\:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
+      - "http://SERVERNAMEPORT/dataset"
+      - "http://SERVERNAMEPORT/model"
+      - "http://SERVERNAMEPORT/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
diff --git a/aa-server.yaml b/aa-server.yaml
index 260c72e..5ca2b72 100644
--- a/aa-server.yaml
+++ b/aa-server.yaml
@@ -15,25 +15,25 @@
 # Exceptions:
   :free_uris: #request-method for uri not controlled by A&A
     ? - :GET
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
-      - "http://SERVERNAME/model"
-      - "http://SERVERNAME/dataset"
-      - "http://SERVERNAME/validation"
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/resources/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
+      - "http://SERVERNAMEPORT/model"
+      - "http://SERVERNAMEPORT/dataset"
+      - "http://SERVERNAMEPORT/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/resources/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVER\/compound/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/compound/
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/task/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVER\/algorithm/
-      - "http://SERVERNAME/dataset"
-      - "http://SERVERNAME/model"
-      - "http://SERVERNAME/validation"
-      - !ruby/regexp /http\:\/\/ESCAPEDSERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
+      - "http://SERVERNAMEPORT/dataset"
+      - "http://SERVERNAMEPORT/model"
+      - "http://SERVERNAMEPORT/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
diff --git a/config.sh b/config.sh
index ae90af3..dcd4db3 100755
--- a/config.sh
+++ b/config.sh
@@ -22,6 +22,7 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="localhost"
 WWW_DEST="$OT_PREFIX/www"
+PORT="" # leave empty for port 80 otherwise set to e.g. ":8080"
 
 # Done.
 
diff --git a/nginx.conf b/nginx.conf
index c89efe2..4dcf81a 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -8,14 +8,14 @@ http {
 
     server_names_hash_bucket_size  256;
 
-    passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
-    passenger_ruby RUBY_DEST/bin/ruby;
-    passenger_default_user USER;
+    passenger_root /home/ot0/opentox-ruby/ruby-enterprise-1.8.7-2011.03/lib/ruby/gems/1.8/gems/passenger-3.0.9;
+    passenger_ruby /home/ot0/opentox-ruby/ruby-enterprise-1.8.7-2011.03/bin/ruby;
+    passenger_default_user ot0;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
 
-    include       NGINX_DEST/conf/mime.types;
+    include       /home/ot0/opentox-ruby/nginx/conf/mime.types;
     default_type  application/octet-stream;
 
     sendfile        on;
@@ -23,11 +23,11 @@ http {
 
     # webservices
     server {
-      listen 80;
+      listen PORT;
       client_max_body_size 5000m;
-      server_name SERVERNAME;
+      server_name toxcreate3;
       location / {
-        root WWW_DEST;
+        root /home/ot0/opentox-ruby/www;
         passenger_enabled on;
       }
       passenger_base_uri /compound;
diff --git a/nginx.sh b/nginx.sh
index 800165e..3a872bc 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -53,6 +53,11 @@ servername=`hostname`
 $GIT checkout nginx.conf>>$LOG 2>&1
 cmd="sed -i -e \"s,PASSENGER,$passenger,;s,SERVERNAME,$servername,;s,RUBY_DEST,$RUBY_DEST,;s,NGINX_DEST,$NGINX_DEST,;s,WWW_DEST,$WWW_DEST,\" ./nginx.conf" && run_cmd "$cmd" "Config"
 cmd="sed -i -e \"s,USER,`whoami`,\" ./nginx.conf" && run_cmd "$cmd" "User"
+PORT=`echo "$PORT" | sed 's/^.//g'`
+if [ -z "$PORT" ]; then
+  PORT=80
+fi
+cmd="sed -i -e \"s,PORT,$PORT,\" ./nginx.conf" && run_cmd "$cmd" "Port"
 cmd="cp ./nginx.conf \"$NGINX_DEST/conf\"" && run_cmd "$cmd" "Copy"
 
 if [ ! -f $NGINX_CONF ]; then
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 70d502b..03d6316 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -71,8 +71,8 @@ mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1
 $GIT checkout production.yaml      >>$LOG 2>&1
 $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
 
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
diff --git a/production.yaml b/production.yaml
index 09efad0..d133cd0 100644
--- a/production.yaml
+++ b/production.yaml
@@ -2,13 +2,13 @@
 
 :services:
 # make sure to enter a full uri (including training slash)
-  opentox-compound:      "http://SERVERNAME/compound/"
-  opentox-dataset:       "http://SERVERNAME/dataset/"
-  opentox-algorithm:     "http://SERVERNAME/algorithm/"
-  opentox-model:         "http://SERVERNAME/model/"
-  opentox-task:          "http://SERVERNAME/task/"
-  opentox-toxcreate:     "http://SERVERNAME/toxcreate/"
-  opentox-validation:    "http://SERVERNAME/validation/"
+  opentox-compound:      "http://SERVERNAMEPORT/compound/"
+  opentox-dataset:       "http://SERVERNAMEPORT/dataset/"
+  opentox-algorithm:     "http://SERVERNAMEPORT/algorithm/"
+  opentox-model:         "http://SERVERNAMEPORT/model/"
+  opentox-task:          "http://SERVERNAMEPORT/task/"
+  opentox-toxcreate:     "http://SERVERNAMEPORT/toxcreate/"
+  opentox-validation:    "http://SERVERNAMEPORT/validation/"
   opentox-ontology:      "http://apps.ideaconsult.net:8080/ontology"
 
 :json_hosts:
-- 
cgit v1.2.3


From 4f89b9975ba06d9e2fffe862b3a12978cab5155b Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 15 Nov 2011 14:28:49 +0100
Subject: Minor fixes

---
 base-install.sh | 2 +-
 config.sh       | 4 ++--
 nginx.conf      | 2 +-
 openbabel.sh    | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/base-install.sh b/base-install.sh
index 373df1f..90abb6e 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -27,7 +27,7 @@ fi
 touch $OT_UI_CONF
 
 # Pkgs
-packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline5-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 sun-java6-jdk wget xsltproc zlib1g-dev"
+packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 sun-java6-jdk wget xsltproc zlib1g-dev"
 
 echo
 echo "Base Packages:"
diff --git a/config.sh b/config.sh
index dcd4db3..e0b20e0 100755
--- a/config.sh
+++ b/config.sh
@@ -20,9 +20,9 @@ KL_NUM_VER="0.9-11"
 REDIS_NUM_VER="2.2.2"
 
 # 4) Server settings.
-NGINX_SERVERNAME="localhost"
+NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT="" # leave empty for port 80 otherwise set to e.g. ":8080"
+PORT=":8080" # leave empty for port 80 otherwise set to e.g. ":8080"
 
 # Done.
 
diff --git a/nginx.conf b/nginx.conf
index 4dcf81a..6ee1662 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -23,7 +23,7 @@ http {
 
     # webservices
     server {
-      listen PORT;
+      listen 8080;
       client_max_body_size 5000m;
       server_name toxcreate3;
       location / {
diff --git a/openbabel.sh b/openbabel.sh
index 4e55ff8..4b6cfc0 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -76,7 +76,7 @@ fi
 echo "Bindings:"
 OB_DONE=false
 . "$OT_UI_CONF"
-mkdir "$OB_DEST_BINDINGS">/dev/null 2>&1
+mkdir -p "$OB_DEST_BINDINGS">/dev/null 2>&1
 if [ ! -d "$OB_DEST_BINDINGS" ]; then
   echo "Install directory '$OB_DEST_BINDINGS' is not available! Aborting..."
   exit 1
-- 
cgit v1.2.3


From 1835d2c61269c1025dac1ba1c5ed5a940cfaa5ff Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 15 Nov 2011 14:53:00 +0100
Subject: Removed sudo

---
 README | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/README b/README
index 79c6569..64efe39 100644
--- a/README
+++ b/README
@@ -18,8 +18,8 @@ Even if we officially support only *one* distro (currently Debian 6.0.1), I test
 After running the installer, configure the system by editing the startup file of your favorite shell (in my case, BASH with the file ~ /. bashrc) to include ~/.opentox-ui.sh (in my case with 'source ...'). This file is the only one that the installer creates outside OT_PREFIX. Thus, the system is fully configured: If you now open a new shell, all environment variables will be adjusted.
 
 To start the system I run the following (but that is not part of the installer):
-sudo nohup $HOME/opentox-ruby/redis-2.2.2/src/redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf &
-sudo nohup $HOME/opentox-ruby/nginx/sbin/nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf &
+nohup $HOME/opentox-ruby/redis-2.2.2/src/redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf &
+nohup $HOME/opentox-ruby/nginx/sbin/nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf &
 
 To uninstall the system simply delete the link from the startup file: Done. To save disc space delete directory OT_PREFIX.
 Anyone can run multiple Opentox versions on the same machine: Just install again, but to a different OT_PREFIX. The switch works manually: Include the sh_<Package>_ot.sh files from the desired OT_PREFIX in $HOME/opentox-ui.sh (only one installation may be activated  at any time).
@@ -76,11 +76,11 @@ otupdate() {
 # Start the server
 otstart() {
   otkill
-  sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  sudo bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
-  if ! pgrep nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
-  if ! pgrep redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
+  if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
+  if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
 }
 
 # Display log
@@ -91,14 +91,14 @@ alias ottail='tail -f $HOME/.opentox/log/production.log'
 
 # Reload the server
 otreload() {
-  sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
 }
 
 # Kill the server
 otkill() {
-  sudo killall nginx >/dev/null 2>&1
-  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  killall nginx >/dev/null 2>&1
+  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
   while ps ax | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while ps ax | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  for p in `pgrep R 2>/dev/null`; do sudo kill -9 $p; done
+  for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
 }
-- 
cgit v1.2.3


From 5c62ba3b7b259f25729d2f0d651147627e141cf8 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 15 Nov 2011 15:34:07 +0100
Subject: Search full name in gem list

---
 opentox-ruby.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 03d6316..7da9263 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -39,7 +39,7 @@ echo
 echo "Opentox-ruby ('$LOG'):"
 
 for mygem in opentox-ruby builder jeweler; do
-  if ! $GEM list | grep "$mygem" >/dev/null 2>&1; then
+  if ! $GEM list | sed 's/\ .*//g' | grep -x "$mygem" >/dev/null 2>&1; then
     cmd="$GEM install $mygem" && run_cmd "$cmd" "$mygem"
   fi
 done
-- 
cgit v1.2.3


From 8dd7e636e80f3024ba059d3b1fb46db534436363 Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Wed, 16 Nov 2011 09:21:24 +0100
Subject: Better hint for colons

---
 config.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.sh b/config.sh
index e0b20e0..cdc0309 100755
--- a/config.sh
+++ b/config.sh
@@ -22,7 +22,7 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT=":8080" # leave empty for port 80 otherwise set to e.g. ":8080"
+PORT="" # set to empty string ("") for port 80 otherwise set to port *using colons* e.g. ":8080"
 
 # Done.
 
-- 
cgit v1.2.3


From 3246032fbd4b04b1e944bf6d2239dec5c48872f2 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 09:32:47 +0100
Subject: Added hint to pubkey at github

---
 config.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.sh b/config.sh
index cdc0309..e7415b3 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, master)
+OT_BRANCH="development"     # Maturity              (development -you need SSH key at Github-, master)
 
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
-- 
cgit v1.2.3


From 4c578f36fded69cfe49fd00f6dea8013a6cba4bd Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Wed, 16 Nov 2011 10:41:22 +0100
Subject: Fixed PORT in nginx.conf

---
 config.sh  | 3 ++-
 nginx.conf | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/config.sh b/config.sh
index cdc0309..222cd7a 100755
--- a/config.sh
+++ b/config.sh
@@ -8,6 +8,7 @@
 OT_DIST="debian"       # Linux distribution    (debian)
 OT_INSTALL="local"     # Type                  (gem, local, server)
 OT_BRANCH="development"     # Maturity              (development, master)
+# NOTE: For branches other than 'master' you have to have your public SSH key at Github and must be a member of 'opentox-ruby' group.
 
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
@@ -22,7 +23,7 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT="" # set to empty string ("") for port 80 otherwise set to port *using colons* e.g. ":8080"
+PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colons* e.g. ":8080"
 
 # Done.
 
diff --git a/nginx.conf b/nginx.conf
index 6ee1662..4dcf81a 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -23,7 +23,7 @@ http {
 
     # webservices
     server {
-      listen 8080;
+      listen PORT;
       client_max_body_size 5000m;
       server_name toxcreate3;
       location / {
-- 
cgit v1.2.3


From e675838dffb7826da8e71fa2b692afe6ef1d0869 Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Wed, 16 Nov 2011 11:00:05 +0100
Subject: Fixed otkill: only my processes

---
 README | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README b/README
index 64efe39..7d06d5c 100644
--- a/README
+++ b/README
@@ -98,7 +98,7 @@ otreload() {
 otkill() {
   killall nginx >/dev/null 2>&1
   bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
-  while ps ax | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  while ps ax | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
 }
-- 
cgit v1.2.3


From 2ddf9dd65a657a3ecf5a636e8e3f66fad581ab6a Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Wed, 16 Nov 2011 11:18:15 +0100
Subject: Fixed nginx.conf

---
 nginx.conf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nginx.conf b/nginx.conf
index 4dcf81a..4372940 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -8,14 +8,14 @@ http {
 
     server_names_hash_bucket_size  256;
 
-    passenger_root /home/ot0/opentox-ruby/ruby-enterprise-1.8.7-2011.03/lib/ruby/gems/1.8/gems/passenger-3.0.9;
-    passenger_ruby /home/ot0/opentox-ruby/ruby-enterprise-1.8.7-2011.03/bin/ruby;
-    passenger_default_user ot0;
+    passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
+    passenger_ruby RUBY_DEST/bin/ruby;
+    passenger_default_user USER;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
 
-    include       /home/ot0/opentox-ruby/nginx/conf/mime.types;
+    include       NGINX_DEST/conf/mime.types;
     default_type  application/octet-stream;
 
     sendfile        on;
@@ -25,9 +25,9 @@ http {
     server {
       listen PORT;
       client_max_body_size 5000m;
-      server_name toxcreate3;
+      server_name SERVERNAME;
       location / {
-        root /home/ot0/opentox-ruby/www;
+        root WWW_DEST;
         passenger_enabled on;
       }
       passenger_base_uri /compound;
-- 
cgit v1.2.3


From 28d4c0a14a8f4b66d9d0f03e55097c22280b8fdd Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 12:42:16 +0100
Subject: Fixed branch keeping

---
 README | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/README b/README
index 7d06d5c..db3b9c0 100644
--- a/README
+++ b/README
@@ -31,12 +31,12 @@ otconfig() {
   source $HOME/.opentox-ui.sh
 }
 
-# Update the development version
+# Update the version
 otupdate() {
   START_DIR=`pwd`
   otconfig
   cd $HOME/opentox-ruby/www/opentox
-  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo $d ; cd $d ; git pull  ; echo ; cd - ;  done
+  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ;  done
   cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
   mv libbbrc/Makefile libbbrc/Makefile~
   mv liblast/Makefile liblast/Makefile~
@@ -102,3 +102,4 @@ otkill() {
   while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
 }
+
-- 
cgit v1.2.3


From 69fa1d589bce1d6b17ea9948cce3cb80a7f84819 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 13:47:03 +0100
Subject: Added support for OHM port

---
 config.sh       | 3 ++-
 opentox-ruby.sh | 4 ++--
 production.yaml | 2 ++
 redis.sh        | 4 ++++
 4 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/config.sh b/config.sh
index 9d227ef..9ebd47d 100755
--- a/config.sh
+++ b/config.sh
@@ -22,7 +22,8 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colons* e.g. ":8080"
+PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
+OHM_PORT="6379" # set to port (no colon)
 
 # Done.
 
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index 7da9263..f6fa077 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -71,8 +71,8 @@ mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1
 $GIT checkout production.yaml      >>$LOG 2>&1
 $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
 
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
diff --git a/production.yaml b/production.yaml
index d133cd0..709b133 100644
--- a/production.yaml
+++ b/production.yaml
@@ -17,6 +17,8 @@
   - "webservices.in-silico.ch"
   - "opentox.informatik.uni-freiburg.de"
 
+:ohm_port: OHM_PORT
+
 # Uncomment for verbose logging
 LOGGER
 :logger: debug
diff --git a/redis.sh b/redis.sh
index 2f55539..a670cff 100755
--- a/redis.sh
+++ b/redis.sh
@@ -59,6 +59,10 @@ if ! $REDIS_DONE; then
   if ! grep "save 900 1" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then 
     echo "save 900 1" >> $REDIS_SERVER_CONF 2>$LOG
   fi
+
+  if ! grep "port $OHM_PORT" $REDIS_SERVER_CONF >>$LOG 2>&1 ; then 
+    echo "port $OHM_PORT" >> $REDIS_SERVER_CONF 2>$LOG
+  fi
 fi
 
 if [ ! -f $REDIS_CONF ]; then
-- 
cgit v1.2.3


From 483d87ed8064573f60194f7936701d21f8728e61 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 15:21:07 +0100
Subject: Fixed PORT to NGINX_PORT

---
 aa-server.yaml  | 30 +++++++++++++++---------------
 config.sh       |  4 ++--
 nginx.conf      | 12 ++++++------
 nginx.sh        |  8 ++++----
 opentox-ruby.sh |  4 ++--
 production.yaml | 14 +++++++-------
 6 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/aa-server.yaml b/aa-server.yaml
index 5ca2b72..aa08799 100644
--- a/aa-server.yaml
+++ b/aa-server.yaml
@@ -15,25 +15,25 @@
 # Exceptions:
   :free_uris: #request-method for uri not controlled by A&A
     ? - :GET
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
-      - "http://SERVERNAMEPORT/model"
-      - "http://SERVERNAMEPORT/dataset"
-      - "http://SERVERNAMEPORT/validation"
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/resources/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
+      - "http://SERVERNAMENGINX_PORT/model"
+      - "http://SERVERNAMENGINX_PORT/dataset"
+      - "http://SERVERNAMENGINX_PORT/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/compound/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
-      - "http://SERVERNAMEPORT/dataset"
-      - "http://SERVERNAMEPORT/model"
-      - "http://SERVERNAMEPORT/validation"
-      - !ruby/regexp /http\:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
+      - "http://SERVERNAMENGINX_PORT/dataset"
+      - "http://SERVERNAMENGINX_PORT/model"
+      - "http://SERVERNAMENGINX_PORT/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
diff --git a/config.sh b/config.sh
index 9ebd47d..a50b05b 100755
--- a/config.sh
+++ b/config.sh
@@ -22,8 +22,8 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
-OHM_PORT="6379" # set to port (no colon)
+NGINX_PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
+OHM_PORT="6380" # set to port (no colon)
 
 # Done.
 
diff --git a/nginx.conf b/nginx.conf
index 4372940..6a8186a 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -8,14 +8,14 @@ http {
 
     server_names_hash_bucket_size  256;
 
-    passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
-    passenger_ruby RUBY_DEST/bin/ruby;
-    passenger_default_user USER;
+    passenger_root /home/am/opentox-ruby/ruby-enterprise-1.8.7-2011.03/lib/ruby/gems/1.8/gems/passenger-3.0.9;
+    passenger_ruby /home/am/opentox-ruby/ruby-enterprise-1.8.7-2011.03/bin/ruby;
+    passenger_default_user am;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
 
-    include       NGINX_DEST/conf/mime.types;
+    include       /home/am/opentox-ruby/nginx/conf/mime.types;
     default_type  application/octet-stream;
 
     sendfile        on;
@@ -25,9 +25,9 @@ http {
     server {
       listen PORT;
       client_max_body_size 5000m;
-      server_name SERVERNAME;
+      server_name z21mn;
       location / {
-        root WWW_DEST;
+        root /home/am/opentox-ruby/www;
         passenger_enabled on;
       }
       passenger_base_uri /compound;
diff --git a/nginx.sh b/nginx.sh
index 3a872bc..32efc96 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -53,11 +53,11 @@ servername=`hostname`
 $GIT checkout nginx.conf>>$LOG 2>&1
 cmd="sed -i -e \"s,PASSENGER,$passenger,;s,SERVERNAME,$servername,;s,RUBY_DEST,$RUBY_DEST,;s,NGINX_DEST,$NGINX_DEST,;s,WWW_DEST,$WWW_DEST,\" ./nginx.conf" && run_cmd "$cmd" "Config"
 cmd="sed -i -e \"s,USER,`whoami`,\" ./nginx.conf" && run_cmd "$cmd" "User"
-PORT=`echo "$PORT" | sed 's/^.//g'`
-if [ -z "$PORT" ]; then
-  PORT=80
+NGINX_PORT=`echo "$NGINX_PORT" | sed 's/^.//g'`
+if [ -z "$NGINX_PORT" ]; then
+  NGINX_PORT=80
 fi
-cmd="sed -i -e \"s,PORT,$PORT,\" ./nginx.conf" && run_cmd "$cmd" "Port"
+cmd="sed -i -e \"s,NGINX_PORT,$NGINX_PORT,\" ./nginx.conf" && run_cmd "$cmd" "NGINX_PORT"
 cmd="cp ./nginx.conf \"$NGINX_DEST/conf\"" && run_cmd "$cmd" "Copy"
 
 if [ ! -f $NGINX_CONF ]; then
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index f6fa077..ec7f5c2 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -71,8 +71,8 @@ mkdir -p "$HOME/.opentox/tmp" >>$LOG 2>&1
 $GIT checkout production.yaml      >>$LOG 2>&1
 $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
 
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
-cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,PORT,$PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
+cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
diff --git a/production.yaml b/production.yaml
index 709b133..e0f39d4 100644
--- a/production.yaml
+++ b/production.yaml
@@ -2,13 +2,13 @@
 
 :services:
 # make sure to enter a full uri (including training slash)
-  opentox-compound:      "http://SERVERNAMEPORT/compound/"
-  opentox-dataset:       "http://SERVERNAMEPORT/dataset/"
-  opentox-algorithm:     "http://SERVERNAMEPORT/algorithm/"
-  opentox-model:         "http://SERVERNAMEPORT/model/"
-  opentox-task:          "http://SERVERNAMEPORT/task/"
-  opentox-toxcreate:     "http://SERVERNAMEPORT/toxcreate/"
-  opentox-validation:    "http://SERVERNAMEPORT/validation/"
+  opentox-compound:      "http://SERVERNAMENGINX_PORT/compound/"
+  opentox-dataset:       "http://SERVERNAMENGINX_PORT/dataset/"
+  opentox-algorithm:     "http://SERVERNAMENGINX_PORT/algorithm/"
+  opentox-model:         "http://SERVERNAMENGINX_PORT/model/"
+  opentox-task:          "http://SERVERNAMENGINX_PORT/task/"
+  opentox-toxcreate:     "http://SERVERNAMENGINX_PORT/toxcreate/"
+  opentox-validation:    "http://SERVERNAMENGINX_PORT/validation/"
   opentox-ontology:      "http://apps.ideaconsult.net:8080/ontology"
 
 :json_hosts:
-- 
cgit v1.2.3


From 21240d7fad96d6e2205f497f44de16a4658e4516 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 15:23:04 +0100
Subject: Fixed PORT to NGINX_PORT

---
 aa-local.yaml | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/aa-local.yaml b/aa-local.yaml
index 5ca2b72..aa08799 100644
--- a/aa-local.yaml
+++ b/aa-local.yaml
@@ -15,25 +15,25 @@
 # Exceptions:
   :free_uris: #request-method for uri not controlled by A&A
     ? - :GET
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
-      - "http://SERVERNAMEPORT/model"
-      - "http://SERVERNAMEPORT/dataset"
-      - "http://SERVERNAMEPORT/validation"
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/resources/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
+      - "http://SERVERNAMENGINX_PORT/model"
+      - "http://SERVERNAMENGINX_PORT/dataset"
+      - "http://SERVERNAMENGINX_PORT/validation"
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/resources/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
     ? - :GET
       - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
-      - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/compound/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/toxcreate\/[a-z,A-Z,\/,_\-]*$/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
+      - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/compound/
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/task/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
-    : - !ruby/regexp /http:\/\/ESCAPEDSERVERPORT\/algorithm/
-      - "http://SERVERNAMEPORT/dataset"
-      - "http://SERVERNAMEPORT/model"
-      - "http://SERVERNAMEPORT/validation"
-      - !ruby/regexp /http\:\/\/ESCAPEDSERVERPORT\/validation\/[a-z,A-Z,\/,_\-]*$/
+    : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/algorithm/
+      - "http://SERVERNAMENGINX_PORT/dataset"
+      - "http://SERVERNAMENGINX_PORT/model"
+      - "http://SERVERNAMENGINX_PORT/validation"
+      - !ruby/regexp /http\:\/\/ESCAPEDSERVERNGINX_PORT\/validation\/[a-z,A-Z,\/,_\-]*$/
-- 
cgit v1.2.3


From 80115dd66a89823fac1dac4690a6c8e87b530a2b Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 15:25:00 +0100
Subject: Fixed PORT to NGINX_PORT

---
 nginx.conf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nginx.conf b/nginx.conf
index 6a8186a..0ff4dec 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -23,7 +23,7 @@ http {
 
     # webservices
     server {
-      listen PORT;
+      listen NGINX_PORT;
       client_max_body_size 5000m;
       server_name z21mn;
       location / {
-- 
cgit v1.2.3


From 18880d3774f9f93cba7341f93498ca33fdabc169 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 16:03:14 +0100
Subject: Fixed PORT to NGINX_PORT

---
 nginx.conf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nginx.conf b/nginx.conf
index 0ff4dec..9f87adf 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -8,14 +8,14 @@ http {
 
     server_names_hash_bucket_size  256;
 
-    passenger_root /home/am/opentox-ruby/ruby-enterprise-1.8.7-2011.03/lib/ruby/gems/1.8/gems/passenger-3.0.9;
-    passenger_ruby /home/am/opentox-ruby/ruby-enterprise-1.8.7-2011.03/bin/ruby;
-    passenger_default_user am;
+    passenger_root RUBY_DEST/lib/ruby/gems/1.8/gems/PASSENGER;
+    passenger_ruby RUBY_DEST/bin/ruby;
+    passenger_default_user USER;
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
 
-    include       /home/am/opentox-ruby/nginx/conf/mime.types;
+    include       NGINX_DEST/conf/mime.types;
     default_type  application/octet-stream;
 
     sendfile        on;
@@ -25,9 +25,9 @@ http {
     server {
       listen NGINX_PORT;
       client_max_body_size 5000m;
-      server_name z21mn;
+      server_name SERVERNAME;
       location / {
-        root /home/am/opentox-ruby/www;
+        root WWW_DEST;
         passenger_enabled on;
       }
       passenger_base_uri /compound;
-- 
cgit v1.2.3


From ecb20ea48a05feb74f86408ccd27ecc274d08080 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 17:20:46 +0100
Subject: Separate file for ot-tools

---
 README           | 84 ++++----------------------------------------------------
 ot-tools-user.sh | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 85 insertions(+), 79 deletions(-)
 create mode 100644 ot-tools-user.sh

diff --git a/README b/README
index db3b9c0..00ed726 100644
--- a/README
+++ b/README
@@ -13,7 +13,11 @@ Here are some of my goals when writing the installer:
 - Encapsulated (everything is installed in a sub-directory in $HOME)
 - Logged (all non-elemtary actions are logged)
 
-Even if we officially support only *one* distro (currently Debian 6.0.1), I tested the installer successfully on various Ubuntus. In the README at the top are the requirements of the installer. By default, everything is installed to $HOME/opentox-ruby (=OT_PREFIX). The configs go to OT_PREFIX/.sh_<Package>_ot.sh for each package.
+
+Configure your system in config.sh. 
+NOTE for variable NGINX_PORT: leave this empty or set to ":80" to use port 80. If you do this, use the ot-scripts in "ot-tools-root.sh". Otherwise, if NGINX_PORT >1024, use ot-scripts in "ot-tools-user.sh".
+
+Even if we officially support only *one* distro (currently Debian 6.0.1), I tested the installer successfully on various Ubuntus. In this README at the top are the requirements of the installer. By default, everything is installed to $HOME/opentox-ruby (=OT_PREFIX). The configs go to OT_PREFIX/.sh_<Package>_ot.sh for each package.
 
 After running the installer, configure the system by editing the startup file of your favorite shell (in my case, BASH with the file ~ /. bashrc) to include ~/.opentox-ui.sh (in my case with 'source ...'). This file is the only one that the installer creates outside OT_PREFIX. Thus, the system is fully configured: If you now open a new shell, all environment variables will be adjusted.
 
@@ -24,82 +28,4 @@ nohup $HOME/opentox-ruby/nginx/sbin/nginx -c $HOME/opentox-ruby/nginx/conf/nginx
 To uninstall the system simply delete the link from the startup file: Done. To save disc space delete directory OT_PREFIX.
 Anyone can run multiple Opentox versions on the same machine: Just install again, but to a different OT_PREFIX. The switch works manually: Include the sh_<Package>_ot.sh files from the desired OT_PREFIX in $HOME/opentox-ui.sh (only one installation may be activated  at any time).
 
-Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
-
-# Load server config
-otconfig() {
-  source $HOME/.opentox-ui.sh
-}
-
-# Update the version
-otupdate() {
-  START_DIR=`pwd`
-  otconfig
-  cd $HOME/opentox-ruby/www/opentox
-  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ;  done
-  cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
-  mv libbbrc/Makefile libbbrc/Makefile~
-  mv liblast/Makefile liblast/Makefile~
-  if ! git pull; then
-    echo "Error! Pull for Fminer failed."
-    return 1
-  fi
-  mv libbbrc/Makefile~ libbbrc/Makefile
-  mv liblast/Makefile~ liblast/Makefile
-  make -C libbbrc/ clean
-  make -C libbbrc/ ruby
-  make -C liblast/ clean
-  make -C liblast/ ruby
-  cd -
-  cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
-  if ! git pull; then
-    echo "Error! Pull for Last-Utils failed."
-    return 1
-  fi
-  cd -
-  cd opentox-ruby
-  LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
-  if [ -h $LINK_DIR ]; then 
-    rm -f $LINK_DIR
-  fi
-  rake install
-  if ! [ -h $LINK_DIR ]; then
-    echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
-    rm -rf "$LINK_DIR~"
-    mv "$LINK_DIR" "$LINK_DIR~"
-    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}`
-  fi
-  echo "Please execute 'otstart' to restart."
-  cd "$START_DIR"
-}
-
-# Start the server
-otstart() {
-  otkill
-  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
-  sleep 2
-  if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
-  if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
-}
-
-# Display log
-alias otless='less $HOME/.opentox/log/production.log'
-
-# Tail log
-alias ottail='tail -f $HOME/.opentox/log/production.log'
-
-# Reload the server
-otreload() {
-  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
-}
-
-# Kill the server
-otkill() {
-  killall nginx >/dev/null 2>&1
-  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
-  while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
-  for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
-}
 
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
new file mode 100644
index 0000000..64f26d3
--- /dev/null
+++ b/ot-tools-user.sh
@@ -0,0 +1,80 @@
+# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
+# USE ONLY IF YOUR NGINX PORT IS >1024 (NOT PRIVILEGED)
+
+# Load server config
+otconfig() {
+  source $HOME/.opentox-ui.sh
+}
+
+# Update the version
+otupdate() {
+  START_DIR=`pwd`
+  otconfig
+  cd $HOME/opentox-ruby/www/opentox
+  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ;  done
+  cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
+  mv libbbrc/Makefile libbbrc/Makefile~
+  mv liblast/Makefile liblast/Makefile~
+  if ! git pull; then
+    echo "Error! Pull for Fminer failed."
+    return 1
+  fi
+  mv libbbrc/Makefile~ libbbrc/Makefile
+  mv liblast/Makefile~ liblast/Makefile
+  make -C libbbrc/ clean
+  make -C libbbrc/ ruby
+  make -C liblast/ clean
+  make -C liblast/ ruby
+  cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
+  if ! git pull; then
+    echo "Error! Pull for Last-Utils failed."
+    return 1
+  fi
+  cd -
+  cd opentox-ruby
+  LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
+  if [ -h $LINK_DIR ]; then 
+    rm -f $LINK_DIR
+  fi
+  rake install
+  if ! [ -h $LINK_DIR ]; then
+    echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
+    rm -rf "$LINK_DIR~"
+    mv "$LINK_DIR" "$LINK_DIR~"
+    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}`
+  fi
+  echo "Please execute 'otstart' to restart."
+  cd "$START_DIR"
+}
+
+# Start the server
+otstart() {
+  otkill
+  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  sleep 2
+  if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
+  if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
+}
+
+# Display log
+alias otless='less $HOME/.opentox/log/production.log'
+
+# Tail log
+alias ottail='tail -f $HOME/.opentox/log/production.log'
+
+# Reload the server
+otreload() {
+  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+}
+
+# Kill the server
+otkill() {
+  killall nginx >/dev/null 2>&1
+  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
+}
+
-- 
cgit v1.2.3


From 47cdf2243d076ade575894fdefe14f99107e2160 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 17:30:08 +0100
Subject: Using separate files for ot-tools

---
 README           |  3 +--
 ot-tools-root.sh | 79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 80 insertions(+), 2 deletions(-)
 create mode 100644 ot-tools-root.sh

diff --git a/README b/README
index 00ed726..7828109 100644
--- a/README
+++ b/README
@@ -14,8 +14,7 @@ Here are some of my goals when writing the installer:
 - Logged (all non-elemtary actions are logged)
 
 
-Configure your system in config.sh. 
-NOTE for variable NGINX_PORT: leave this empty or set to ":80" to use port 80. If you do this, use the ot-scripts in "ot-tools-root.sh". Otherwise, if NGINX_PORT >1024, use ot-scripts in "ot-tools-user.sh".
+Configure your system in config.sh. NOTE for variable NGINX_PORT: leave this empty or set to ":80" to use port 80. If you do this, use the ot-scripts in "ot-tools-root.sh". Otherwise, if NGINX_PORT >1024, use ot-scripts in "ot-tools-user.sh".
 
 Even if we officially support only *one* distro (currently Debian 6.0.1), I tested the installer successfully on various Ubuntus. In this README at the top are the requirements of the installer. By default, everything is installed to $HOME/opentox-ruby (=OT_PREFIX). The configs go to OT_PREFIX/.sh_<Package>_ot.sh for each package.
 
diff --git a/ot-tools-root.sh b/ot-tools-root.sh
new file mode 100644
index 0000000..eec6780
--- /dev/null
+++ b/ot-tools-root.sh
@@ -0,0 +1,79 @@
+# Some useful scripts to put in your ~/.bashrc in case you are using bash (assuming OT_PREFIX is '~/opentox-ruby'):
+# USE ONLY IF YOUR NGINX PORT IS less or equal to 1024 (PRIVILEGED)
+
+# Load server config
+otconfig() {
+  source $HOME/.opentox-ui.sh
+}
+
+# Update the version
+otupdate() {
+  START_DIR=`pwd`
+  otconfig
+  cd $HOME/opentox-ruby/www/opentox
+  for d in `find -not -name "." -type d -maxdepth 1 2>/dev/null`; do echo ; echo $d ; cd $d ; MYBRANCH=`git branch | grep "*" | sed 's/.*\ //g'`; git pull origin $MYBRANCH ; cd - ;  done
+  cd  $HOME/opentox-ruby/www/opentox/algorithm/libfminer
+  mv libbbrc/Makefile libbbrc/Makefile~
+  mv liblast/Makefile liblast/Makefile~
+  if ! git pull; then
+    echo "Error! Pull for Fminer failed."
+    return 1
+  fi
+  mv libbbrc/Makefile~ libbbrc/Makefile
+  mv liblast/Makefile~ liblast/Makefile
+  make -C libbbrc/ clean
+  make -C libbbrc/ ruby
+  make -C liblast/ clean
+  make -C liblast/ ruby
+  cd -
+  cd $HOME/opentox-ruby/www/opentox/algorithm/last-utils
+  if ! git pull; then
+    echo "Error! Pull for Last-Utils failed."
+    return 1
+  fi
+  cd -
+  cd opentox-ruby
+  LINK_DIR=`gem which opentox-ruby | sed 's/\/opentox-ruby.rb//'`
+  if [ -h $LINK_DIR ]; then 
+    rm -f $LINK_DIR
+  fi
+  rake install
+  if ! [ -h $LINK_DIR ]; then
+    echo "Warning! Your lib $LINK_DIR is no symlink. Linking back for you..."
+    rm -rf "$LINK_DIR~"
+    mv "$LINK_DIR" "$LINK_DIR~"
+    ln -sf $HOME/opentox-ruby/www/opentox/opentox-ruby/lib `echo ${LINK_DIR::${#LINK_DIR}-3}`
+  fi
+  echo "Please execute 'otstart' to restart."
+  cd "$START_DIR"
+}
+
+# Start the server
+otstart() {
+  otkill
+  sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  sudo bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  sleep 2
+  if ! pgrep -u root nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
+  if ! pgrep -u root redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
+}
+
+# Display log
+alias otless='less $HOME/.opentox/log/production.log'
+
+# Tail log
+alias ottail='tail -f $HOME/.opentox/log/production.log'
+
+# Reload the server
+otreload() {
+  sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+}
+
+# Kill the server
+otkill() {
+  sudo killall -u root nginx >/dev/null 2>&1
+  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
+  for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done
+}
-- 
cgit v1.2.3


From 7776175ac7166537408d30e6a8f7210f8e9a9a3d Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 16 Nov 2011 17:41:40 +0100
Subject: Port 80 default

---
 config.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.sh b/config.sh
index 9ebd47d..1886f89 100755
--- a/config.sh
+++ b/config.sh
@@ -22,7 +22,7 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT=":8081" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
+PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
 OHM_PORT="6379" # set to port (no colon)
 
 # Done.
-- 
cgit v1.2.3


From 5017e2f3b8865db62c2420cd0101426a46a8714f Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 09:00:16 +0100
Subject: Fixed nginx installer

---
 nginx.sh | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nginx.sh b/nginx.sh
index 32efc96..ed8a3df 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -53,12 +53,15 @@ servername=`hostname`
 $GIT checkout nginx.conf>>$LOG 2>&1
 cmd="sed -i -e \"s,PASSENGER,$passenger,;s,SERVERNAME,$servername,;s,RUBY_DEST,$RUBY_DEST,;s,NGINX_DEST,$NGINX_DEST,;s,WWW_DEST,$WWW_DEST,\" ./nginx.conf" && run_cmd "$cmd" "Config"
 cmd="sed -i -e \"s,USER,`whoami`,\" ./nginx.conf" && run_cmd "$cmd" "User"
-NGINX_PORT=`echo "$NGINX_PORT" | sed 's/^.//g'`
+
 if [ -z "$NGINX_PORT" ]; then
   NGINX_PORT=80
+else
+  NGINX_PORT=`echo "$NGINX_PORT" | sed 's/^.//g'`
 fi
 cmd="sed -i -e \"s,NGINX_PORT,$NGINX_PORT,\" ./nginx.conf" && run_cmd "$cmd" "NGINX_PORT"
 cmd="cp ./nginx.conf \"$NGINX_DEST/conf\"" && run_cmd "$cmd" "Copy"
+$GIT checkout nginx.conf>>$LOG 2>&1
 
 if [ ! -f $NGINX_CONF ]; then
   echo "if ! echo \"\$PATH\" | grep \"$NGINX_DEST\">/dev/null 2>&1; then export PATH=$NGINX_DEST/sbin:\$PATH; fi" >> "$NGINX_CONF"
-- 
cgit v1.2.3


From 025e9ed0ef3aae6cfd0b0f3c2c2e122d50ac008d Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 09:14:48 +0100
Subject: Re-enabled OB_DONE, always using public checkout

---
 openbabel.sh           | 22 +++++++++++-----------
 opentox-webservices.sh |  6 +-----
 2 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/openbabel.sh b/openbabel.sh
index 4b6cfc0..3d45f00 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -86,15 +86,15 @@ else
   fi
 fi
 
-#if ! $OB_DONE ; then
-  OB_SRC_DIR="/tmp/$OB_VER/scripts/ruby/"
-  cd "$OB_SRC_DIR"
-  cmd="ruby extconf.rb --with-openbabel-include=$OB_DEST/include/openbabel-2.0 --with-openbabel-lib=$OB_DEST/lib" && run_cmd "$cmd" "Code"
-  cmd="make" && run_cmd "$cmd" "Make"
-  cmd="cp openbabel.so $OB_DEST_BINDINGS" && run_cmd "$cmd" "Install"
-  cmd="ln -sf $OB_DEST_BINDINGS/openbabel.so $RUBY_DEST/lib/ruby/site_ruby/1.8/`uname -m`-linux/" && run_cmd "$cmd" "Link"
-  cd "$DIR"
-  . "`pwd`/utils.sh"
-  cmd="ruby test-ob-rb.rb" && run_cmd "$cmd" "Load"
-#fi
+if ! $OB_DONE ; then
+ OB_SRC_DIR="/tmp/$OB_VER/scripts/ruby/"
+ cd "$OB_SRC_DIR"
+ cmd="ruby extconf.rb --with-openbabel-include=$OB_DEST/include/openbabel-2.0 --with-openbabel-lib=$OB_DEST/lib" && run_cmd "$cmd" "Code"
+ cmd="make" && run_cmd "$cmd" "Make"
+ cmd="cp openbabel.so $OB_DEST_BINDINGS" && run_cmd "$cmd" "Install"
+ cmd="ln -sf $OB_DEST_BINDINGS/openbabel.so $RUBY_DEST/lib/ruby/site_ruby/1.8/`uname -m`-linux/" && run_cmd "$cmd" "Link"
+ cd "$DIR"
+ . "`pwd`/utils.sh"
+ cmd="ruby test-ob-rb.rb" && run_cmd "$cmd" "Load"
+fi
 
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index ef98ded..c4fbd16 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -46,11 +46,7 @@ mkdir -p "$WWW_DEST/opentox" >>$LOG 2>&1
 cd "$WWW_DEST/opentox" >>$LOG 2>&1
 for s in compound dataset algorithm model toxcreate task validation; do
     rm -rf "$s" >>$LOG 2>&1
-    if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
-      $GIT clone "git@github.com:opentox/$s.git" "$s" >>$LOG 2>&1
-    else
-      $GIT clone "git://github.com/opentox/$s.git" "$s" >>$LOG 2>&1
-    fi
+    $GIT clone "git://github.com/opentox/$s.git" "$s" >>$LOG 2>&1
     cd "$s" >>$LOG 2>&1
     $GIT checkout -b $OT_BRANCH origin/$OT_BRANCH >>$LOG 2>&1
     #rm -rf public >>$LOG 2>&1
-- 
cgit v1.2.3


From 64e21f3e1916c989786a2c329e922f7932e330ee Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 09:36:12 +0100
Subject: Fixed otkill (ohm port)

---
 ot-tools-root.sh | 2 +-
 ot-tools-user.sh | 2 +-
 redis.sh         | 1 +
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index eec6780..b6ebfcc 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -72,7 +72,7 @@ otreload() {
 # Kill the server
 otkill() {
   sudo killall -u root nginx >/dev/null 2>&1
-  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
   while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 64f26d3..ede3d7b 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -72,7 +72,7 @@ otreload() {
 # Kill the server
 otkill() {
   killall nginx >/dev/null 2>&1
-  bash -c "source $HOME/.opentox-ui.sh; redis-cli shutdown >/dev/null 2>&1"
+  bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
   while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
diff --git a/redis.sh b/redis.sh
index a670cff..ad3b695 100755
--- a/redis.sh
+++ b/redis.sh
@@ -67,6 +67,7 @@ fi
 
 if [ ! -f $REDIS_CONF ]; then
   echo "if ! echo \"\$PATH\" | grep \"$REDIS_DEST\">/dev/null 2>&1; then export PATH=$REDIS_DEST/src:\$PATH; fi" >> "$REDIS_CONF"
+  echo "export OHM_PORT=$OHM_PORT" >> "$REDIS_CONF"
   echo "Redis configuration has been stored in '$REDIS_CONF'."
 
   if ! grep ". \"$REDIS_CONF\"" $OT_UI_CONF; then
-- 
cgit v1.2.3


From 6857244ddd2fd79f2a8f70341227e7ebdcf34b05 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 10:02:47 +0100
Subject: Fixed otconfig in ot-functions

---
 ot-tools-root.sh | 11 +++++++----
 ot-tools-user.sh | 11 +++++++----
 2 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index b6ebfcc..7e1233b 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -50,9 +50,10 @@ otupdate() {
 
 # Start the server
 otstart() {
+  otconfig
   otkill
-  sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  sudo bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  sudo bash -c "nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  sudo bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
   if ! pgrep -u root nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
   if ! pgrep -u root redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
@@ -66,13 +67,15 @@ alias ottail='tail -f $HOME/.opentox/log/production.log'
 
 # Reload the server
 otreload() {
-  sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+  otconfig
+  sudo bash -c "nginx -s reload"
 }
 
 # Kill the server
 otkill() {
+  otconfig
   sudo killall -u root nginx >/dev/null 2>&1
-  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
+  sudo bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
   while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index ede3d7b..1ad02f4 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -50,9 +50,10 @@ otupdate() {
 
 # Start the server
 otstart() {
+  otconfig
   otkill
-  bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  bash -c "nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
   if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
   if ! pgrep -u $USER redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
@@ -66,13 +67,15 @@ alias ottail='tail -f $HOME/.opentox/log/production.log'
 
 # Reload the server
 otreload() {
-  bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
+  otconfig
+  bash -c "nginx -s reload"
 }
 
 # Kill the server
 otkill() {
+  otconfig
   killall nginx >/dev/null 2>&1
-  bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
+  bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
   while ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u $USER R 2>/dev/null`; do kill -9 $p; done
-- 
cgit v1.2.3


From 6f7c4d138916a12d9aab0fc4cad8c4d6b472742b Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 13:17:55 +0100
Subject: Fixed deletion of /tmp/passenger

---
 install | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install b/install
index 6a1e84f..9dee38c 100755
--- a/install
+++ b/install
@@ -16,7 +16,7 @@ echo
 cmd="sudo echo -n \"\"" && run_cmd "$cmd" "Acquire privileges"
 
 echo "Cleaning up /tmp files."
-sudo rm -rf /tmp/openbabel* /tmp/kernlab* /tmp/ruby* /tmp/passenger* 
+sudo rm -rf /tmp/openbabel* /tmp/kernlab* /tmp/ruby*
 
 . "./base-install.sh"
 . "./ruby.sh"
-- 
cgit v1.2.3


From d231bd32f9be394119fa877b1b059a79986ee050 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 17 Nov 2011 13:44:31 +0100
Subject: Fixed NGINX_PORT string

---
 config.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config.sh b/config.sh
index 1886f89..60dff2a 100755
--- a/config.sh
+++ b/config.sh
@@ -22,7 +22,7 @@ REDIS_NUM_VER="2.2.2"
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
 WWW_DEST="$OT_PREFIX/www"
-PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
+NGINX_PORT="" # set to empty string ("") for port 80 otherwise set to port *using colon* e.g. ":8080"
 OHM_PORT="6379" # set to port (no colon)
 
 # Done.
-- 
cgit v1.2.3


From d2bf668856c63e2682aba0df3a504a1bac6ec7f3 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 21 Nov 2011 12:57:53 +0100
Subject: Installer stores tmp files in $HOME/tmp and backups the existing
 system.

---
 install                | 31 ++++++++++++++++++++++++++++---
 kernlab.sh             |  4 ++--
 nginx.sh               |  2 +-
 openbabel.sh           | 10 +++++-----
 opentox-ruby.sh        |  2 +-
 opentox-webservices.sh |  2 +-
 redis.sh               |  2 +-
 ruby.sh                |  8 ++++----
 8 files changed, 43 insertions(+), 18 deletions(-)

diff --git a/install b/install
index 9dee38c..88ef63e 100755
--- a/install
+++ b/install
@@ -7,7 +7,32 @@ if [ "$(id -u)" = "0" ]; then
   exit 1
 fi
 
-LOG="/tmp/`basename $0`-log.txt"
+echo
+echo "Warning! If all IST services are stoppped press return, else <Ctrl+C> to stop installation."
+echo "Note: Your data will be backupped."
+read help_var
+echo 
+
+mkdir -p $HOME/tmp/
+if [ -f "$HOME/.opentox-ui.sh" ]
+then
+  mv -b -v $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh~
+else
+  echo "$HOME/.opentox-ui.sh does not exist."
+fi
+if [ -d "$HOME/.opentox" ]
+then
+  mv -b -v -T $HOME/.opentox $HOME/.opentox~
+else
+  echo "$HOME/.opentox does not exist."
+fi
+if [ -d "$HOME/opentox-ruby" ]
+then
+  mv -b -v -T $HOME/opentox-ruby $HOME/opentox-ruby~
+else
+  echo "$HOME/opentox-ruby does not exist."
+fi 
+LOG="$HOME/tmp/`basename $0`-log.txt"
 . "./utils.sh"
 echo
 echo "Opentox-ruby installation."
@@ -15,8 +40,8 @@ echo "You may need to give root password for some privileged actions right now a
 echo
 cmd="sudo echo -n \"\"" && run_cmd "$cmd" "Acquire privileges"
 
-echo "Cleaning up /tmp files."
-sudo rm -rf /tmp/openbabel* /tmp/kernlab* /tmp/ruby*
+echo "Cleaning up $HOME/tmp files."
+rm -rf $HOME/tmp/openbabel* $HOME/tmp/kernlab* $HOME/tmp/ruby*
 
 . "./base-install.sh"
 . "./ruby.sh"
diff --git a/kernlab.sh b/kernlab.sh
index 2fba2a8..511874b 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -26,7 +26,7 @@ if [ ! -e "$R" ]; then
 fi
 
 # Pkg
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Kernlab ('$LOG')."
@@ -46,7 +46,7 @@ fi
 
 
 if ! $R_DONE; then
-  cd /tmp
+  cd $HOME/tmp
   URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download"
 
diff --git a/nginx.sh b/nginx.sh
index ed8a3df..cb8c6b6 100755
--- a/nginx.sh
+++ b/nginx.sh
@@ -26,7 +26,7 @@ if [ ! -e "$GIT" ]; then
 fi
 
 
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Nginx ('$LOG'):"
diff --git a/openbabel.sh b/openbabel.sh
index 3d45f00..3016d95 100755
--- a/openbabel.sh
+++ b/openbabel.sh
@@ -21,7 +21,7 @@ if [ ! -e "$WGET" ]; then
 fi
 
 # Pkg
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Openbabel ('$OB_DEST', '$LOG'):"
@@ -38,13 +38,13 @@ else
 fi
 
 if [ ! $OB_DONE ]; then
-  cd "/tmp">>$LOG 2>/dev/null
+  cd "$HOME/tmp">>$LOG 2>/dev/null
   URI="http://downloads.sourceforge.net/project/openbabel/openbabel/$OB_NUM_VER/$OB_VER.tar.gz?use_mirror=kent"
-  if ! [ -d "/tmp/$OB_VER" ]; then 
+  if ! [ -d "$HOME/tmp/$OB_VER" ]; then 
     cmd="$WGET $URI" && run_cmd "$cmd" "Download"
     cmd="tar zxf $OB_VER.tar.gz?use_mirror=kent $OB_VER"  && run_cmd "$cmd" "Unpack"
   fi
-  cd "/tmp/$OB_VER">>$LOG 2>/dev/null
+  cd "$HOME/tmp/$OB_VER">>$LOG 2>/dev/null
 
   cmd="./configure --prefix=$OB_DEST" && run_cmd "$cmd" "Configure"
   cmd="make" && run_cmd "$cmd" "Make"
@@ -87,7 +87,7 @@ else
 fi
 
 if ! $OB_DONE ; then
- OB_SRC_DIR="/tmp/$OB_VER/scripts/ruby/"
+ OB_SRC_DIR="$HOME/tmp/$OB_VER/scripts/ruby/"
  cd "$OB_SRC_DIR"
  cmd="ruby extconf.rb --with-openbabel-include=$OB_DEST/include/openbabel-2.0 --with-openbabel-lib=$OB_DEST/lib" && run_cmd "$cmd" "Code"
  cmd="make" && run_cmd "$cmd" "Make"
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index ec7f5c2..9705682 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -33,7 +33,7 @@ fi
 
 
 # Pkg
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Opentox-ruby ('$LOG'):"
diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index c4fbd16..cc53d04 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -37,7 +37,7 @@ if [ ! -e "$RUBY" ]; then
   exit 1
 fi
 
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Webservices ('$LOG'):"
diff --git a/redis.sh b/redis.sh
index ad3b695..f07d119 100755
--- a/redis.sh
+++ b/redis.sh
@@ -19,7 +19,7 @@ if [ ! -e "$WGET" ]; then
   exit 1
 fi
 
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Redis ('$LOG'):"
diff --git a/ruby.sh b/ruby.sh
index a1b8cbe..2e53384 100755
--- a/ruby.sh
+++ b/ruby.sh
@@ -21,7 +21,7 @@ if [ ! -e "$WGET" ]; then
 fi
 
 # Pkg
-LOG="/tmp/`basename $0`-log.txt"
+LOG="$HOME/tmp/`basename $0`-log.txt"
 
 echo
 echo "Ruby Enterprise edition ('$RUBY_DEST', '$LOG')."
@@ -38,13 +38,13 @@ else
 fi
 
 if [ ! $RUBY_DONE ]; then
-  cd /tmp
+  cd $HOME/tmp
   URI="http://rubyenterpriseedition.googlecode.com/files/$RUBY_VER.tar.gz"
-  if ! [ -d "/tmp/$RUBY_VER" ]; then
+  if ! [ -d "$HOME/tmp/$RUBY_VER" ]; then
     cmd="$WGET $URI" && run_cmd "$cmd" "Download"
     cmd="tar xzf $RUBY_VER.tar.gz" && run_cmd "$cmd" "Unpack"
   fi
-  cmd="sh /tmp/$RUBY_VER/installer  --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install"
+  cmd="sh $HOME/tmp/$RUBY_VER/installer  --dont-install-useful-gems --no-dev-docs --auto=$RUBY_DEST" && run_cmd "$cmd" "Install"
 fi
 
 
-- 
cgit v1.2.3


From 066dee09478c87c83951c15cced72e604fb9db3d Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 22 Nov 2011 14:06:34 +0100
Subject: Added ambit_descriptors.yaml

---
 ambit_descriptors.yaml | 124 +++++++++++++++++++++++++++++++++++++++++++++++++
 opentox-ruby.sh        |   1 +
 2 files changed, 125 insertions(+)
 create mode 100644 ambit_descriptors.yaml

diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml
new file mode 100644
index 0000000..19e66f9
--- /dev/null
+++ b/ambit_descriptors.yaml
@@ -0,0 +1,124 @@
+--- 
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor: 
+  :category: "geometrical"
+  :name: "Length Over Breadth"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor: 
+  :category: "topological"
+  :name: "Kier & Hall SMARTS"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor: 
+  :category: "topological"
+  :name: "Fragment Complexity"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor: 
+  :category: "electronic"
+  :name: "Atomic Polarizabilities"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor: 
+  :category: "constitutional"
+  :name: "Largest Chain"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor: 
+  :category: "topological"
+  :name: "Chi Path Indices"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor: 
+  :category: "topological"
+  :name: "Petitjean Number"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor: 
+  :category: "constitutional"
+  :name: "Longest Aliphatic Chain"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor: 
+  :category: "topological"
+  :name: "Kier and Hall kappa molecular shape indices"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor: 
+  :category: "constitutional"
+  :name: "Aromatic Bonds Count"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: 
+  :category: "electronic"
+  :name: "Charged Partial Surface Areas"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: 
+  :category: "topological"
+  :name: "Vertex adjacency information magnitude"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass: 
+  :category: "topological"
+  :name: "Moreau-Broto Autocorrelation (mass) descriptors"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor: 
+  :category: "constitutional"
+  :name: "Lipinski's Rule of Five"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor: 
+  :category: "geometrical"
+  :name: "Gravitational Index"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor: 
+  :category: "topological"
+  :name: "Wiener Numbers"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor: 
+  :category: "topological"
+  :name: "Chi Path-Cluster Indices"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor: 
+  :category: "constitutional"
+  :name: "Atoms Count"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor: 
+  :category: "geometrical"
+  :name: "Moments of Inertia"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor: 
+  :category: "topological"
+  :name: "Carbon Types"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability: 
+  :category: "topological"
+  :name: "Moreau-Broto Autocorrelation (polarizability) descriptors"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor: 
+  :category: "topological"
+  :name: "Eccentric Connectivity Index"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor: 
+  :category: "hybrid"
+  :name: "BCUT"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor: 
+  :category: "constitutional"
+  :name: "Aromatic Atoms Count"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor: 
+  :category: "hybrid"
+  :name: "WHIM"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor: 
+  :category: "constitutional"
+  :name: "ALogP"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor: 
+  :category: "constitutional"
+  :name: "XLogP"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor: 
+  :category: "topological"
+  :name: "Petitjean Number"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor: 
+  :category: "topological"
+  :name: "Molecular Distance Edge"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor: 
+  :category: "topological"
+  :name: "Chi Chain Indices"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor: 
+  :category: "constitutional"
+  :name: "Bonds Count"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor: 
+  :category: "constitutional"
+  :name: "Mannhold LogP"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor: 
+  :category: "electronic"
+  :name: "Bond Polarizabilities"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge: 
+  :category: "topological"
+  :name: "Moreau-Broto Autocorrelation (charge) descriptors"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor: 
+  :category: "topological"
+  :name: "Zagreb Index"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor: 
+  :category: "topological"
+  :name: "Chi Cluster Indices"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor: 
+  :category: "constitutional"
+  :name: "Rotatable Bonds Count"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor: 
+  :category: "topological"
+  :name: "Topological Polar Surface Area"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor: 
+  :category: "electronic"
+  :name: "Hydrogen Bond Donors"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor: 
+  :category: "electronic"
+  :name: "Hydrogen Bond Acceptors"
+http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor: 
+  :category: "constitutional"
+  :name: "Largest Pi Chain"
diff --git a/opentox-ruby.sh b/opentox-ruby.sh
index ec7f5c2..d53d5ba 100755
--- a/opentox-ruby.sh
+++ b/opentox-ruby.sh
@@ -73,6 +73,7 @@ $GIT checkout aa-$OT_INSTALL.yaml  >>$LOG 2>&1
 
 cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" production.yaml > $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 1"
 cmd="sed -e \"s,SERVERNAME,$servername,;s,ESCAPEDSERVER,$escapedserver,;s,LOGGER,$logger,;s,AA,$aa,;s,WWW_DEST,$WWW_DEST,;s,NGINX_PORT,$NGINX_PORT,;s,OHM_PORT,$OHM_PORT,\" aa-$OT_INSTALL.yaml >> $HOME/.opentox/config/production.yaml" && run_cmd "$cmd" "Config 2"
+cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit"
 
 if [ "$OT_BRANCH" = "development" ] || expr match "$OT_BRANCH" "release"; then
   mkdir -p $WWW_DEST/opentox >>$LOG 2>&1
-- 
cgit v1.2.3


From 7acb3bc7db272581b9055c8e073aa7b07206f6fe Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 23 Nov 2011 09:49:21 +0100
Subject: Minor improvements

---
 opentox-webservices.sh |  8 ++++----
 update                 | 16 ----------------
 2 files changed, 4 insertions(+), 20 deletions(-)
 delete mode 100755 update

diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index cc53d04..88f864c 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -65,21 +65,21 @@ cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update"
 cd "libfminer/libbbrc">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-cd -
+cd - >>$LOG 2>&1
 cd "libfminer/liblast">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-cd -
+cd - >>$LOG 2>&1
 for mylib in bbrc last; do
   cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ -I$OB_DEST/include/openbabel-2.0,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile; sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ -L$OB_DEST/lib,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)"
   cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ -I$RUBY_DEST/lib/ruby/1.8/`uname -m`-linux,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)"
 done
 cd "libfminer/libbbrc">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd -
+cd - >>$LOG 2>&1
 cd "libfminer/liblast">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd -
+cd - >>$LOG 2>&1
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
diff --git a/update b/update
deleted file mode 100755
index 77183ed..0000000
--- a/update
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-. /etc/profile
-gem update opentox-ruby
-dir=`pwd`
-cd /var/www/opentox
-for s in *; do
-  echo $s
-  cd $s
-  git pull
-  cd -
-done
-cd /var/www/algorithm
-rake fminer:update
-kill `cat /opt/nginx/logs/nginx.pid`
-/opt/nginx/sbin/nginx
-cd $dir
-- 
cgit v1.2.3


From 0475b661fc3eaaf916a49e9a08aec17be2e94df1 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 23 Nov 2011 09:53:05 +0100
Subject: Minor improvements

---
 opentox-webservices.sh |  8 ++++----
 update                 | 16 ----------------
 2 files changed, 4 insertions(+), 20 deletions(-)
 delete mode 100755 update

diff --git a/opentox-webservices.sh b/opentox-webservices.sh
index cc53d04..88f864c 100755
--- a/opentox-webservices.sh
+++ b/opentox-webservices.sh
@@ -65,21 +65,21 @@ cmd="$GIT submodule update" && run_cmd "$cmd" "Fminer Update"
 cd "libfminer/libbbrc">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-cd -
+cd - >>$LOG 2>&1
 cd "libfminer/liblast">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
-cd -
+cd - >>$LOG 2>&1
 for mylib in bbrc last; do
   cmd="sed -i 's,^INCLUDE_OB.*,INCLUDE_OB\ =\ -I$OB_DEST/include/openbabel-2.0,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile; sed -i 's,^LDFLAGS_OB.*,LDFLAGS_OB\ =\ -L$OB_DEST/lib,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (OB)"
   cmd="sed -i 's,^INCLUDE_RB.*,INCLUDE_RB\ =\ -I$RUBY_DEST/lib/ruby/1.8/`uname -m`-linux,g' $WWW_DEST/opentox/algorithm/libfminer/lib$mylib/Makefile" && run_cmd "$cmd" "Makefile $mylib (RB)"
 done
 cd "libfminer/libbbrc">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make BBRC"
-cd -
+cd - >>$LOG 2>&1
 cd "libfminer/liblast">>$LOG 2>&1
 cmd="make ruby" && run_cmd "$cmd" "Make LAST"
-cd -
+cd - >>$LOG 2>&1
 cd "last-utils">>$LOG 2>&1
 $GIT checkout $OT_BRANCH>>$LOG 2>&1
 $GIT pull >>$LOG 2>&1
diff --git a/update b/update
deleted file mode 100755
index 77183ed..0000000
--- a/update
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-. /etc/profile
-gem update opentox-ruby
-dir=`pwd`
-cd /var/www/opentox
-for s in *; do
-  echo $s
-  cd $s
-  git pull
-  cd -
-done
-cd /var/www/algorithm
-rake fminer:update
-kill `cat /opt/nginx/logs/nginx.pid`
-/opt/nginx/sbin/nginx
-cd $dir
-- 
cgit v1.2.3


From 10937ac1b0e62deb51bf3f2c619ed82a4f89bb62 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Thu, 24 Nov 2011 16:29:25 +0100
Subject: minor improvements

---
 install | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/install b/install
index 88ef63e..705ff44 100755
--- a/install
+++ b/install
@@ -13,24 +13,24 @@ echo "Note: Your data will be backupped."
 read help_var
 echo 
 
-mkdir -p $HOME/tmp/
+mkdir -p $HOME/tmp/ >/dev/null 2>&1
 if [ -f "$HOME/.opentox-ui.sh" ]
 then
   mv -b -v $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh~
 else
-  echo "$HOME/.opentox-ui.sh does not exist."
+  echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
 fi
 if [ -d "$HOME/.opentox" ]
 then
   mv -b -v -T $HOME/.opentox $HOME/.opentox~
 else
-  echo "$HOME/.opentox does not exist."
+  echo "$HOME/.opentox does not found (nothing to backup)."
 fi
 if [ -d "$HOME/opentox-ruby" ]
 then
   mv -b -v -T $HOME/opentox-ruby $HOME/opentox-ruby~
 else
-  echo "$HOME/opentox-ruby does not exist."
+  echo "$HOME/opentox-ruby does not found (nothing to backup)."
 fi 
 LOG="$HOME/tmp/`basename $0`-log.txt"
 . "./utils.sh"
-- 
cgit v1.2.3


From 7d7a277cd3c2a56a044aa5364c3a651e03a60652 Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Wed, 30 Nov 2011 08:52:54 +0100
Subject: Supporting MLR install

---
 kernlab.sh | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/kernlab.sh b/kernlab.sh
index 511874b..8139747 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -45,13 +45,17 @@ else
 fi
 
 
-if ! $R_DONE; then
+if $R_DONE; then
   cd $HOME/tmp
+  export R_LIBS="$KL_DEST" # To install non-global
+
   URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download"
+  cmd="$WGET $URI" && run_cmd "$cmd" "Download KL"
+  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL"
 
-  export R_LIBS="$KL_DEST" # To install non-global
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install"
+  URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
+  cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
+  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS"
 fi
 
 
-- 
cgit v1.2.3


From 582753e3f256b7b9329dd6750731ed7a27ae5b87 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 5 Dec 2011 13:55:49 +0100
Subject: Fixed backup.

---
 install | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/install b/install
index 705ff44..a486660 100755
--- a/install
+++ b/install
@@ -14,21 +14,22 @@ read help_var
 echo 
 
 mkdir -p $HOME/tmp/ >/dev/null 2>&1
+DATE=`date +_%Y%m%d_%H_%M`
 if [ -f "$HOME/.opentox-ui.sh" ]
 then
-  mv -b -v $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh~
+  mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
 else
   echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
 fi
 if [ -d "$HOME/.opentox" ]
 then
-  mv -b -v -T $HOME/.opentox $HOME/.opentox~
+  mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE
 else
   echo "$HOME/.opentox does not found (nothing to backup)."
 fi
 if [ -d "$HOME/opentox-ruby" ]
 then
-  mv -b -v -T $HOME/opentox-ruby $HOME/opentox-ruby~
+  mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE
 else
   echo "$HOME/opentox-ruby does not found (nothing to backup)."
 fi 
-- 
cgit v1.2.3


From d13ae21e492357bb93947998a298bb1a7af1a625 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Mon, 5 Dec 2011 14:01:05 +0100
Subject: Fixed backup.

---
 install | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/install b/install
index 705ff44..a486660 100755
--- a/install
+++ b/install
@@ -14,21 +14,22 @@ read help_var
 echo 
 
 mkdir -p $HOME/tmp/ >/dev/null 2>&1
+DATE=`date +_%Y%m%d_%H_%M`
 if [ -f "$HOME/.opentox-ui.sh" ]
 then
-  mv -b -v $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh~
+  mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
 else
   echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
 fi
 if [ -d "$HOME/.opentox" ]
 then
-  mv -b -v -T $HOME/.opentox $HOME/.opentox~
+  mv -v --backup=numbered -T $HOME/.opentox $HOME/.opentox$DATE
 else
   echo "$HOME/.opentox does not found (nothing to backup)."
 fi
 if [ -d "$HOME/opentox-ruby" ]
 then
-  mv -b -v -T $HOME/opentox-ruby $HOME/opentox-ruby~
+  mv -v --backup=numbered -T $HOME/opentox-ruby $HOME/opentox-ruby$DATE
 else
   echo "$HOME/opentox-ruby does not found (nothing to backup)."
 fi 
-- 
cgit v1.2.3


From 4ad029cf4123a436822bd829a42e87ff9b634ef0 Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Mon, 5 Dec 2011 14:59:31 +0100
Subject: Added RB

---
 kernlab.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/kernlab.sh b/kernlab.sh
index 8139747..52006dc 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -55,7 +55,11 @@ if $R_DONE; then
 
   URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS"
+  cmd="$R CMD INSTALL pls_2.3.0.tar.gz" && run_cmd "$cmd" "Install PLS"
+
+  URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz"
+  cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
+  cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
 fi
 
 
-- 
cgit v1.2.3


From 13218d2158ace60f02d0d2d4b0bbaf4f980c61c3 Mon Sep 17 00:00:00 2001
From: ot1 <andreas@maunz.de>
Date: Mon, 5 Dec 2011 15:00:42 +0100
Subject: Fixed installation of pls

---
 kernlab.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kernlab.sh b/kernlab.sh
index 8139747..4faf08c 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -55,7 +55,7 @@ if $R_DONE; then
 
   URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install PLS"
+  cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
 fi
 
 
-- 
cgit v1.2.3


From 23cd09e039577124fa27b5b0f72509dd058bd308 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 5 Dec 2011 15:25:10 +0100
Subject: Fixed if statement.

---
 kernlab.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kernlab.sh b/kernlab.sh
index 4faf08c..582950f 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -45,7 +45,7 @@ else
 fi
 
 
-if $R_DONE; then
+if ! $R_DONE; then
   cd $HOME/tmp
   export R_LIBS="$KL_DEST" # To install non-global
 
-- 
cgit v1.2.3


From 0924b25654d554a5c6a3fa99e6902227dfe0f6d3 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Wed, 7 Dec 2011 10:30:50 +0100
Subject: Added LEAPS package

---
 kernlab.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/kernlab.sh b/kernlab.sh
index f73d376..3ee6aff 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -60,6 +60,10 @@ if ! $R_DONE; then
   URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
   cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
+
+  URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
+  cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
+  cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS"
 fi
 
 
-- 
cgit v1.2.3


From 4de5abc3c49d8cdb01866f5a038e9a1597fb5ae8 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Fri, 9 Dec 2011 16:39:14 +0100
Subject: Fixed typo

---
 kernlab.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/kernlab.sh b/kernlab.sh
index 3ee6aff..11e5637 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -55,7 +55,7 @@ if ! $R_DONE; then
 
   URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
-  cmd="$R CMD INSTALL pls_2.3.0.tar.gz" && run_cmd "$cmd" "Install PLS"
+  cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
 
   URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
-- 
cgit v1.2.3


From 89658d67203e00dedd2a795fceb61d954d07b2d5 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Sun, 11 Dec 2011 22:17:06 +0100
Subject: Updated download path to new version (robustbase_0.8-0)

---
 kernlab.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/kernlab.sh b/kernlab.sh
index 11e5637..c4fc206 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -57,9 +57,9 @@ if ! $R_DONE; then
   cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
   cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
 
-  URI="http://cran.r-project.org/src/contrib/robustbase_0.7-8.tar.gz"
+  URI="http://cran.r-project.org/src/contrib/robustbase_0.8-0.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
-  cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
+  cmd="$R CMD INSTALL robustbase_0.8-0.tar.gz" && run_cmd "$cmd" "Install RB"
 
   URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
-- 
cgit v1.2.3


From d56d27d7e7804521c8b8dce7c273fbb4e5ddd86c Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 12 Dec 2011 10:58:18 +0100
Subject: Changed download path to archive version

---
 kernlab.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/kernlab.sh b/kernlab.sh
index c4fc206..a833bd9 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -57,9 +57,9 @@ if ! $R_DONE; then
   cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
   cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
 
-  URI="http://cran.r-project.org/src/contrib/robustbase_0.8-0.tar.gz"
+  URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
-  cmd="$R CMD INSTALL robustbase_0.8-0.tar.gz" && run_cmd "$cmd" "Install RB"
+  cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
 
   URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
   cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
-- 
cgit v1.2.3


From 600466723755e0440fff0f908bfddc2ef3f05fa5 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 12 Dec 2011 11:43:08 +0100
Subject: Removed static download url for r packages. They have to be
 downloaded manually (only temporarily).

---
 kernlab.sh | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/kernlab.sh b/kernlab.sh
index a833bd9..c4bafbd 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -53,16 +53,20 @@ if ! $R_DONE; then
   cmd="$WGET $URI" && run_cmd "$cmd" "Download KL"
   cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL"
 
-  URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
+
+  echo "Warning! If you already downloaded pls_2.3-0.tar.gz , robustbase_0.7-8.tar.gz and leaps_2.9.tar.gz from http://cran.r-project.org/src/contrib/ into $HOME/tmp/ press return, else <Ctrl+C> to stop installation."
+  read help_var2
+  echo 
+  #URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
+  #cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
   cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
 
-  URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
+  #URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz"
+  #cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
   cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
 
-  URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
+  #URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
+  #cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
   cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS"
 fi
 
-- 
cgit v1.2.3


From 73747676c8afa6188c87ea6795f3db940ab59b9c Mon Sep 17 00:00:00 2001
From: am <am@z21mn.(none)>
Date: Tue, 20 Dec 2011 11:22:58 +0100
Subject: Fixed bugs 1., 2., 6. of http://goo.gl/1InHw

---
 base-install.sh | 2 +-
 config.sh       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/base-install.sh b/base-install.sh
index 90abb6e..5fccec5 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -27,7 +27,7 @@ fi
 touch $OT_UI_CONF
 
 # Pkgs
-packs="binutils build-essential git-core gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline-dev libsqlite3-dev libssl-dev libxml2-dev libxslt1-dev lsb-release psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 sun-java6-jdk wget xsltproc zlib1g-dev"
+packs="binutils build-essential git-core 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 wget xsltproc zlib1g-dev"
 
 echo
 echo "Base Packages:"
diff --git a/config.sh b/config.sh
index 60dff2a..87b19b7 100755
--- a/config.sh
+++ b/config.sh
@@ -11,13 +11,13 @@ OT_BRANCH="development"     # Maturity              (development -you need SSH k
 
 # 2) Where all binaries are installed.
 OT_PREFIX="$HOME/opentox-ruby"
-OT_JAVA_HOME="/usr/lib/jvm/java-6-sun"
+OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
 
 # 3) What versions to install.
 RUBY_NUM_VER="1.8.7-2011.03"
 OB_NUM_VER="2.2.3"
 KL_NUM_VER="0.9-11"
-REDIS_NUM_VER="2.2.2"
+REDIS_NUM_VER="2.4.4"
 
 # 4) Server settings.
 NGINX_SERVERNAME="toxcreate3.in-silico.ch"
-- 
cgit v1.2.3


From 2ea961e226bb202dc95332c782dd3bc5448e57b3 Mon Sep 17 00:00:00 2001
From: am <am@z21mn.(none)>
Date: Tue, 20 Dec 2011 11:27:01 +0100
Subject: Fixed bug 7. of http://goo.gl/1InHw

---
 ot-tools-user.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index 1ad02f4..57c6c00 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -52,7 +52,7 @@ otupdate() {
 otstart() {
   otconfig
   otkill
-  bash -c "nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
+  bash -c "nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
   bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
   if ! pgrep -u $USER nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
-- 
cgit v1.2.3


From 4a6edd6921869f5ab53acd882f3bff276c31463a Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Thu, 29 Dec 2011 16:19:03 +0100
Subject: cpsa in own category

---
 ambit_descriptors.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ambit_descriptors.yaml b/ambit_descriptors.yaml
index 19e66f9..1e2c347 100644
--- a/ambit_descriptors.yaml
+++ b/ambit_descriptors.yaml
@@ -30,7 +30,7 @@ http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descr
   :category: "constitutional"
   :name: "Aromatic Bonds Count"
 http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor: 
-  :category: "electronic"
+  :category: "cpsa"
   :name: "Charged Partial Surface Areas"
 http://apps.ideaconsult.net:8080/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor: 
   :category: "topological"
-- 
cgit v1.2.3


From 2da57e942972fcfe85ad3bf0671ab82e128fb292 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Fri, 13 Jan 2012 14:05:16 +0100
Subject: fixed search param -S for already installed packs

---
 base-install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/base-install.sh b/base-install.sh
index 5fccec5..73c9e37 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -34,7 +34,7 @@ echo "Base Packages:"
 
 pack_arr=""
 for p in $packs; do
-  if $DPKG -s "$p" >/dev/null 2>&1; then
+  if $DPKG -S "$p" >/dev/null 2>&1; then
      printf "%50s%30s\n" "'$p'" "Y"
   else
      printf "%50s%30s\n" "'$p'" "N"
-- 
cgit v1.2.3


From b6fb537437568bdf274451554663d8273151ffe8 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Mon, 16 Jan 2012 13:12:26 +0100
Subject: fixed search param -S for already installed packs

---
 base-install.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/base-install.sh b/base-install.sh
index 90abb6e..a1ee2bf 100644
--- a/base-install.sh
+++ b/base-install.sh
@@ -34,7 +34,7 @@ echo "Base Packages:"
 
 pack_arr=""
 for p in $packs; do
-  if $DPKG -s "$p" >/dev/null 2>&1; then
+  if $DPKG -S "$p" >/dev/null 2>&1; then
      printf "%50s%30s\n" "'$p'" "Y"
   else
      printf "%50s%30s\n" "'$p'" "N"
-- 
cgit v1.2.3


From 33babc8050bf00dba4929cb35d65bef926c9b7b4 Mon Sep 17 00:00:00 2001
From: micha <micha@tpad.(none)>
Date: Mon, 16 Jan 2012 19:00:36 +0100
Subject: Task cleanup method

---
 aa-local.yaml  | 2 ++
 aa-server.yaml | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/aa-local.yaml b/aa-local.yaml
index aa08799..75cccd0 100644
--- a/aa-local.yaml
+++ b/aa-local.yaml
@@ -29,6 +29,8 @@
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
     : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
+    ? - :DELETE
+    : - "http://SERVERNAMENGINX_PORT/task/cleanup"
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
diff --git a/aa-server.yaml b/aa-server.yaml
index aa08799..75cccd0 100644
--- a/aa-server.yaml
+++ b/aa-server.yaml
@@ -29,6 +29,8 @@
       - !ruby/regexp /sign_(in|out)$/
     ? - :PUT
     : - !ruby/regexp /http:\/\/ESCAPEDSERVERNGINX_PORT\/task/
+    ? - :DELETE
+    : - "http://SERVERNAMENGINX_PORT/task/cleanup"
 
   :authorize_exceptions: #request-method for uri only authenticated, no authorization
     ? - :POST
-- 
cgit v1.2.3


From 2e53016f91abb5af7e9cd24f336fce5f121c92ae Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 31 Jan 2012 09:04:16 +0100
Subject: Adjusted R installation

---
 config.sh  |  4 ++--
 kernlab.sh | 46 ++++++++++++++--------------------------------
 2 files changed, 16 insertions(+), 34 deletions(-)

diff --git a/config.sh b/config.sh
index 60dff2a..b553594 100755
--- a/config.sh
+++ b/config.sh
@@ -34,7 +34,7 @@ RUBY_CONF="$OT_PREFIX/.sh_ruby_ot"
 REDIS_CONF="$OT_PREFIX/.sh_redis_ot"
 NGINX_CONF="$OT_PREFIX/.sh_nginx_ot"
 OB_CONF="$OT_PREFIX/.sh_OB_ot"
-KL_CONF="$OT_PREFIX/.sh_R_ot"
+R_CONF="$OT_PREFIX/.sh_R_ot"
 
 RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
@@ -44,7 +44,7 @@ REDIS_VER="$REDIS_NUM_VER"
 RUBY_DEST="$OT_PREFIX/$RUBY_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
-KL_DEST="$OT_PREFIX/r-packages"
+R_DEST="$OT_PREFIX/r-packages"
 NGINX_DEST="$OT_PREFIX/nginx"
 REDIS_DEST="$OT_PREFIX/redis-$REDIS_VER"
 
diff --git a/kernlab.sh b/kernlab.sh
index c4bafbd..2df0b8e 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -32,53 +32,35 @@ echo
 echo "Kernlab ('$LOG')."
 
 R_DONE=false
-mkdir "$KL_DEST" >/dev/null 2>&1
-if [ ! -d "$KL_DEST" ]; then
-  echo "Install directory '$KL_DEST' is not available! Aborting..."
+mkdir "$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 "$KL_DEST" >/dev/null 2>&1; then # if not empty this will fail
+  if ! rmdir "$R_DEST" >/dev/null 2>&1; then # if not empty this will fail
     R_DONE=true
   else
-    mkdir "$KL_DEST" >/dev/null 2>&1
+    mkdir "$R_DEST" >/dev/null 2>&1
   fi
 fi
 
 
 if ! $R_DONE; then
   cd $HOME/tmp
-  export R_LIBS="$KL_DEST" # To install non-global
-
-  URI="http://cran.r-project.org/src/contrib/Archive/kernlab/kernlab_$KL_VER.tar.gz"
-  cmd="$WGET $URI" && run_cmd "$cmd" "Download KL"
-  cmd="$R CMD INSTALL kernlab_$KL_VER.tar.gz" && run_cmd "$cmd" "Install KL"
-
-
-  echo "Warning! If you already downloaded pls_2.3-0.tar.gz , robustbase_0.7-8.tar.gz and leaps_2.9.tar.gz from http://cran.r-project.org/src/contrib/ into $HOME/tmp/ press return, else <Ctrl+C> to stop installation."
-  read help_var2
-  echo 
-  #URI="http://cran.r-project.org/src/contrib/pls_2.3-0.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download PLS"
-  cmd="$R CMD INSTALL pls_2.3-0.tar.gz" && run_cmd "$cmd" "Install PLS"
-
-  #URI="http://cran.r-project.org/src/contrib/00Archive/robustbase/robustbase_0.7-8.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download RB"
-  cmd="$R CMD INSTALL robustbase_0.7-8.tar.gz" && run_cmd "$cmd" "Install RB"
-
-  #URI="http://cran.r-project.org/src/contrib/leaps_2.9.tar.gz"
-  #cmd="$WGET $URI" && run_cmd "$cmd" "Download LEAPS"
-  cmd="$R CMD INSTALL leaps_2.9.tar.gz" && run_cmd "$cmd" "Install LEAPS"
+  export R_LIBS="$R_DEST" # To install non-global
+  options(repos="http://mirrors.softliste.de/cran") # set mirror to avoid questioning the user
+  install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
 fi
 
 
-if [ ! -f $KL_CONF ]; then
+if [ ! -f $R_CONF ]; then
 
-  echo "if echo \"\$R_LIBS\" | grep -v \"$KL_DEST\">/dev/null 2>&1; then export R_LIBS=\"$KL_DEST\"; fi" >> "$KL_CONF"
-  echo "if ! [ -d \"$KL_DEST\" ]; then echo \"\$0: '$KL_DEST' is not a directory!\"; fi" >> "$KL_CONF"
-  echo "R package destination has been stored in '$KL_CONF'."
+  echo "if echo \"\$R_LIBS\" | grep -v \"$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" >> "$R_CONF"
+  echo "R package destination has been stored in '$R_CONF'."
 
-  if ! grep "$KL_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
-    echo ". \"$KL_CONF\"" >> $OT_UI_CONF
+  if ! grep "$R_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then
+    echo ". \"$R_CONF\"" >> $OT_UI_CONF
   fi
 
 fi
-- 
cgit v1.2.3


From 9282f0715873f96cf43c23261a808dc00fb78914 Mon Sep 17 00:00:00 2001
From: Andreas Maunz <andreas@maunz.de>
Date: Tue, 31 Jan 2012 10:07:01 +0100
Subject: Fixed R lib install

---
 config.sh  | 2 --
 install    | 6 +++---
 kernlab.sh | 5 ++---
 packs.R    | 6 ++++++
 4 files changed, 11 insertions(+), 8 deletions(-)
 create mode 100644 packs.R

diff --git a/config.sh b/config.sh
index b553594..afe2012 100755
--- a/config.sh
+++ b/config.sh
@@ -16,7 +16,6 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-sun"
 # 3) What versions to install.
 RUBY_NUM_VER="1.8.7-2011.03"
 OB_NUM_VER="2.2.3"
-KL_NUM_VER="0.9-11"
 REDIS_NUM_VER="2.2.2"
 
 # 4) Server settings.
@@ -38,7 +37,6 @@ R_CONF="$OT_PREFIX/.sh_R_ot"
 
 RUBY_VER="ruby-enterprise-$RUBY_NUM_VER"
 OB_VER="openbabel-$OB_NUM_VER"
-KL_VER="$KL_NUM_VER"
 REDIS_VER="$REDIS_NUM_VER"
 
 RUBY_DEST="$OT_PREFIX/$RUBY_VER"
diff --git a/install b/install
index a486660..b0422b5 100755
--- a/install
+++ b/install
@@ -19,19 +19,19 @@ if [ -f "$HOME/.opentox-ui.sh" ]
 then
   mv -v --backup=numbered $HOME/.opentox-ui.sh $HOME/.opentox-ui.sh$DATE
 else
-  echo "$HOME/.opentox-ui.sh does not found (nothing to backup)."
+  echo "$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 "$HOME/.opentox does not found (nothing to backup)."
+  echo "$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 "$HOME/opentox-ruby does not found (nothing to backup)."
+  echo "$HOME/opentox-ruby not found (nothing to backup)."
 fi 
 LOG="$HOME/tmp/`basename $0`-log.txt"
 . "./utils.sh"
diff --git a/kernlab.sh b/kernlab.sh
index 2df0b8e..aad125d 100755
--- a/kernlab.sh
+++ b/kernlab.sh
@@ -46,10 +46,9 @@ fi
 
 
 if ! $R_DONE; then
-  cd $HOME/tmp
   export R_LIBS="$R_DEST" # To install non-global
-  options(repos="http://mirrors.softliste.de/cran") # set mirror to avoid questioning the user
-  install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
+  cmd="$R CMD BATCH packs.R" && run_cmd "$cmd" "R packages"
+  eval "$cmd"
 fi
 
 
diff --git a/packs.R b/packs.R
new file mode 100644
index 0000000..b130360
--- /dev/null
+++ b/packs.R
@@ -0,0 +1,6 @@
+# CRAN package installer for opentox-ruby
+# AM, 2012
+
+# set mirror to avoid questioning the user
+options(repos="http://mirrors.softliste.de/cran")
+install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
-- 
cgit v1.2.3


From ca56463e893e0d058dc5571e673d2fbfe14508b2 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Thu, 9 Feb 2012 09:29:22 +0100
Subject: Added R packages: "randomForest","RANN"

---
 packs.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/packs.R b/packs.R
index b130360..b6b1930 100644
--- a/packs.R
+++ b/packs.R
@@ -3,4 +3,4 @@
 
 # set mirror to avoid questioning the user
 options(repos="http://mirrors.softliste.de/cran")
-install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape"))
+install.packages(c("caret", "doMC", "e1071", "foreach", "iterators", "kernlab", "multicore", "plyr", "reshape", "randomForest", "RANN"))
-- 
cgit v1.2.3


From dc9337579e3a1f04bd3da39eafc598e99e945f8f Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 14 Feb 2012 11:41:31 +0100
Subject: Fixed PATH problem and replaced redis version.

---
 ot-tools-root.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index 7e1233b..a46293a 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -52,8 +52,8 @@ otupdate() {
 otstart() {
   otconfig
   otkill
-  sudo bash -c "nohup redis-server $HOME/opentox-ruby/redis-2.2.2/redis.conf >/dev/null 2>&1 &"
-  sudo bash -c "nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
+  sudo bash -c "source $HOME/.opentox-ui.sh; nohup redis-server $HOME/opentox-ruby/redis-*/redis.conf >/dev/null 2>&1 &"
+  sudo bash -c "source $HOME/.opentox-ui.sh; nohup nginx -c $HOME/opentox-ruby/nginx/conf/nginx.conf >/dev/null 2>&1 &"
   sleep 2
   if ! pgrep -u root nginx>/dev/null 2>&1; then echo "Failed to start nginx."; fi
   if ! pgrep -u root redis-server>/dev/null 2>&1; then echo "Failed to start redis."; fi
-- 
cgit v1.2.3


From 6f754e8504fbf1f47339f5485b01820833d5e2a1 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 14 Feb 2012 12:06:22 +0100
Subject: Fixed PATH problem in otreload.

---
 ot-tools-root.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index a46293a..da3bd69 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -68,7 +68,7 @@ alias ottail='tail -f $HOME/.opentox/log/production.log'
 # Reload the server
 otreload() {
   otconfig
-  sudo bash -c "nginx -s reload"
+  sudo bash -c "source $HOME/.opentox-ui.sh; nginx -s reload"
 }
 
 # Kill the server
-- 
cgit v1.2.3


From 50faf0c3cbd7ce76fa388e9207a1e9993fd450f7 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Tue, 14 Feb 2012 12:10:06 +0100
Subject: Fixed PATH problem in otkill

---
 ot-tools-root.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ot-tools-root.sh b/ot-tools-root.sh
index da3bd69..064ea29 100644
--- a/ot-tools-root.sh
+++ b/ot-tools-root.sh
@@ -75,7 +75,7 @@ otreload() {
 otkill() {
   otconfig
   sudo killall -u root nginx >/dev/null 2>&1
-  sudo bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
+  sudo bash -c "source $HOME/.opentox-ui.sh; redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1"
   while sudo ps x | grep PassengerWatchdog | grep -v grep >/dev/null 2>&1; do sleep 1; done
   while sudo ps x | grep Rack | grep -v grep >/dev/null 2>&1; do sleep 1; done
   for p in `pgrep -u root R 2>/dev/null`; do sudo kill -9 $p; done
-- 
cgit v1.2.3


From 803ae809cc5092e082ee527dac6eb25c1a63dcf3 Mon Sep 17 00:00:00 2001
From: rautenberg <rautenberg@in-silico.ch>
Date: Thu, 1 Mar 2012 10:07:49 +0100
Subject: add passenger_max_pool_size to nginx.conf with value 30

---
 nginx.conf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nginx.conf b/nginx.conf
index 9f87adf..c15dc02 100644
--- a/nginx.conf
+++ b/nginx.conf
@@ -14,6 +14,7 @@ http {
     passenger_log_level 2;
     passenger_spawn_method conservative;
     #passenger_use_global_queue on;
+    passenger_max_pool_size 30;
 
     include       NGINX_DEST/conf/mime.types;
     default_type  application/octet-stream;
-- 
cgit v1.2.3