Updates and details.

1 files changed, 55 insertions, 21 deletions

diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md
index a76f0af..3a4859d 100644
--- a/_posts/2012-08-09-install-opentox-development-environment.md
+++ b/_posts/2012-08-09-install-opentox-development-environment.md
@@ -7,54 +7,80 @@ tags: [deployment, installation, Ubuntu, Debian, Setup]
 ---
 {% include JB/setup %}
 
-HowTo install recent opentox services on Ubuntu or Debian
+How To install recent opentox services on Ubuntu or Debian
 
 # Installation:
 
-Installation (`development` at the point of writing this = 09/08/2012) is tested with Debian 6.0.5 and should work with recent Ubuntu versions. Installer is available at github. Please follow instruction (an internet connection is required):
+Installation (`development` at the point of writing this = 15/08/2012) is tested with Debian 6.0.5 and should work with recent Ubuntu versions. Installer is available at [github](https://github.com/opentox/install). Please follow instruction (an internet connection is required):
 
+    # Check if "sudo" is available (e.g. sudo ls)
+    # Install git
     sudo apt-get install git-core 
-    # please add you ssh keys at github. You may add your name/email adress to the local git config.
-    cd ~
-    git clone git@github.com:opentox/install.git
-    cd install
+    # Please add your ssh key at github via https://github.com/. 
+    # You may add your name/email address to the local git config.
+    # Download the installer from github. 
+    git clone git@github.com:opentox/install.git $HOME/install
+    cd $HOME/install
     git checkout development
-    # check config.sh
+    # First check config.sh
     ./install
 
-This installation script will prepare your system for the opentox services, including installing necessary dependencies, opentox config, raptor, rasqal and 4store. 
+This installation script will prepare your system for the use of `opentox` web services, including installing necessary dependencies, `opentox` config, `raptor`, `rasqal` and `4store`. 
 
 # Install opentox services
 
-    cd $OT_PREFIX # check path in config.sh 
+    # Check OT_PREFIX in $HOME/install/config.sh 
+    OT_PREFIX="path/to/directory"
     # Download opentox-client opentox-server opentox-test algorithm dataset feature and task
-    for f in opentox-client opentox-server opentox-test algorithm dataset feature task; do git clone "git@github.com:opentox/$f.git"; cd $f; git checkout development; git checkout migration; cd ..; done 
-    # install services with script (bundle)
+    for f in opentox-client opentox-server opentox-test algorithm dataset feature task; do 
+      git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
+      cd $OT_PREFIX/$f
+      git checkout development
+      git checkout migration
+    done 
+    # Install services with script (bundle)
     cd $OT_PREFIX/opentox-client/bin 
     ./opentox-client-install 
-    # this script might fail after installing ruby, please start script again. Will be fixed soon.
+    # This script might fail after installing ruby, please start script again. Will be fixed soon.
     cd $OT_PREFIX/opentox-server/bin
     ./opentox-server-install
     cd $OT_PREFIX
-    for f in algorithm dataset feature task opentox-test; do cd $f/bin; ./$f-install; cd ../..; done
-    if ! cat $HOME/.opentox/config/default.rb | grep "compound">/dev/null 2>&1; then echo '$compound = { :uri => "http://webservices.in-silico.ch/compound" }' >> $HOME/.opentox/config/default.rb; fi    
+    for f in algorithm dataset feature task opentox-test; do
+      cd $OT_PREFIX/$f/bin
+      ./$f-install
+    done
+    if ! cat $HOME/.opentox/config/default.rb | grep "compound">/dev/null 2>&1; then i
+      echo '$compound = { :uri => "http://webservices.in-silico.ch/compound" }' >> $HOME/.opentox/config/default.rb
+    fi 
+
+Now, `opentox` web services are downloaded, installed and configured.   
     
-# Add ot-tools to your .bashrc
+# Activate and use ot-tools
 
-    echo '. ~/install/ot-tools-user.sh' >> ~/.bashrc
+Add ot-tools to your .bashrc:
+
+    echo '. ~/.opentox/ot-tools.sh' >> ~/.bashrc
     # source .bashrc or restart shell
 
-# Run services
+All ot-tools (`otconfig`, `otstart`, `otcheck`, `otreload`, `otkill`) are available in your shell. General usage: 
+
+    [otstart|otcheck|otreload|otkill] [all|algorithm|compound|dataset|feature|model|task|validation|4store]
+
+Only `otconfig` does not need an argument, it sets the environment variables for all services. 
+
+Start all services with:
 
     otstart all 
 
-# Kill services 
+Kill all services with:
     
     otkill all
 
+It is possible to manage single services (e.g. `otstart dataset` to run dataset web service). 
+
 # Access web services
 
-The default port setting (see default config file ~/.opentox/conf/default.rb):
+The default port setting (see default config file ~/.opentox/config/default.rb):
 
     Algorithm: localhost:8081/algorithm
     Compound: localhost:8082/compound
@@ -63,13 +89,21 @@ The default port setting (see default config file ~/.opentox/conf/default.rb):
     Model: localhost:8085/model
     Task: localhost:8086/task
     Validation: localhost:8087/validation
-    4store: localhost:8088/status
+    4store: localhost:8088/
+
+NOTE: Only installed service uris are set in the config files. Model and validation service are not available yet and an external compound services is used. 
 
 # Testing services
 
-    cp $HOME/.opentox/config/default.rb $HOME/.opentox/config/test.rb  # This is a workaroung, will be fixed soon.
+    cp $HOME/.opentox/config/default.rb $HOME/.opentox/config/test.rb  # This is a workaround, will be fixed soon.
     cd $OT_PREFIX/opentox-test
     otconfig
     ruby opentox-client.rb
 
+The tests are running for some time and will finish with a short report:
+    
+    Finished tests in 50.728600s, 0.7885 tests/s, 3.1935 assertions/s.
+    40 tests, 162 assertions, 0 failures, 0 errors, 0 skips
+
+To test one specific service run its script (ruby [service_name].rb) located in $OT_PREFIX/opentox-test/test.