Merge branch 'master' of github.com:opentox/opentox.github.com

4 files changed, 127 insertions, 49 deletions

diff --git a/_posts/2012-05-25-installation-issues.md b/_posts/2012-05-25-installation-issues.md
index 97db7bb..ea4adb5 100644
--- a/_posts/2012-05-25-installation-issues.md
+++ b/_posts/2012-05-25-installation-issues.md
@@ -19,6 +19,7 @@ Proceed as follows **before installing**.:
     curl -L http://launchpadlibrarian.net/48177999/libgsl0-dev_1.14%2Bdfsg-1_amd64.deb > libgsl0-dev_1.14+dfsg-1_amd64.deb
     curl -L http://launchpadlibrarian.net/48177998/libgsl0ldbl_1.14%2Bdfsg-1_amd64.deb > libgsl0ldbl_1.14+dfsg-1_amd64.deb
     sudo dpkg -i libgsl0-dev_1.14+dfsg-1_amd64.deb
+    sudo dpkg -i libgsl0ldbl_1.14+dfsg-1_amd64.deb
 
 In the above, adjust your architecture to `i386`, if necessary (please use 64 bit software where possible).
 
diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md
index ab1b0d0..160a18a 100644
--- a/_posts/2012-08-09-install-opentox-development-environment.md
+++ b/_posts/2012-08-09-install-opentox-development-environment.md
@@ -2,77 +2,122 @@
 layout: post
 title: "Install opentox development environment"
 description: ""
-category: development
+category: setup
 tags: [deployment, installation, Ubuntu, Debian, Setup]
 ---
 {% include JB/setup %}
 
-How To install recent opentox services on Ubuntu or Debian
+Architecture overview and how to install recent opentox services on Ubuntu or Debian.
 
-# Installation:
+# Philosophy
 
-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):
+The [opentox installer](https://github.com/opentox/install/tree/development) provides a [POSIX](http://en.wikipedia.org/wiki/POSIX) compatible way to prepare Debian-based systems and install ISTs OpenTox compatible web-services and library code. Please report bugs [here](http://github.com/opentox/install).
+
+Apart from some basic Debian packages, no action requires root access. Everything is installed in the user's home directory. Inside it, the installer prepares the base directory (referred to as `OT_PREFIX`) for OpenTox REST services and provides libraries for the installation and shell integration of services. 
+
+Here are some more goals we had in mind when writing the installer:
+
+- Safe (existence of all binaries will be checked before running, apart from GNU Core Utils)
+- Idempotent (multiple execution incurs no changes to the system)
+- Atomic (return value of non-elementary actions asserted to be TRUE)
+- Encapsulated (everything installed in OT_PREFIX)
+- Logged (all non-elementary actions are logged)
+
+Conceptual approach:
+
+1. Configure the installer in config.sh, then run `install`. 
+2. Configure your system by adding a line to the startup file of your favorite shell (e.g. BASH with the file `~/.bashrc`) to read in `~/.opentox/opentox-ui.sh` (e.g. with `source ~/.opentox/opentox-ui.sh`), so any newly started shell will be configured. 
+3. Use the system, in particular by starting webservices (see below). For `bash` users, a set of tools (called `ot-tools`) is available.
+4. To uninstall, simply remove the line from the startup file, that's all. To save disc space also remove directory `OT_PREFIX`. To remove also your configuration, remove `~/.opentox`.
+
+<br>
+<br>
+<hr>
+<br>
+<br>
+
+# Installation
+
+Installation (`development` at the point of writing this = 22/08/2012) is tested with Debian 6.0.5 and Ubuntu 11.04. Installer is available at [github](https://github.com/opentox/install).
+
+Before starting the installation please check if "sudo" is available (e.g. sudo ls), required for base packages.
 
-    # Check if "sudo" is available (e.g. sudo ls)
     # Install git
-    sudo apt-get install git-core 
-    # 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. 
+    sudo apt-get install git 
+
+Please add your ssh key at github via https://github.com/. You may add your name/email address to the local git config.
+
+Download, configure and execute the installer. 
+
     git clone git@github.com:opentox/install.git $HOME/install
     cd $HOME/install
     git checkout development
-    # First check config.sh
+    # First check config.sh with your favorite editor
     ./install
 
-This installation script will prepare your system for the use of `opentox` web 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`, `rbenv`, `ruby` and `4store`. 
 
 # Install opentox services
 
-    # 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 
+Load environment (general)
+
+    . $HOME/.opentox/config/install/config.sh
+    . $OT_PREFIX/install/utils.sh
+    
+Load environment (with bash):
+
+    . $HOME/.opentox/ot-tools.sh
+    otconfig
+
+Next opentox-client and opentox-server will be downloaded and installed.
+    
+    for f in opentox-client opentox-server; do 
       git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
       cd $OT_PREFIX/$f
-      git checkout development
-      git checkout migration
+      git checkout development 2>/dev/null
+      git checkout migration 2>/dev/null
     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.
     cd $OT_PREFIX/opentox-server/bin
     ./opentox-server-install
-    cd $OT_PREFIX
-    for f in algorithm dataset feature task opentox-test; do
-      cd $OT_PREFIX/$f/bin
-      ./$f-install
+
+OpenTox services(algorithm compound dataset feature task opentox-test) and tests will be downloaded and installed. 
+
+    for f in algorithm compound dataset feature task opentox-test; do
+      git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
+      cd $OT_PREFIX/$f
+      git checkout development 2>/dev/null
+      git checkout migration 2>/dev/null
+      if [ -f $OT_PREFIX/$f/bin/$f-install ]; then
+        cd $OT_PREFIX/$f/bin
+        ./$f-install    
+      fi
     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.   
+At this point `opentox` web services have been downloaded, installed and configured.   
     
-# Activate and use ot-tools
+# Activate and use ot-tools if you are using bash
+
+NOTE: ot-tools do require the use of bash shell.
 
 Add ot-tools to your .bashrc:
 
-    echo '. ~/.opentox/ot-tools.sh' >> ~/.bashrc
+    echo '. $HOME/.opentox/ot-tools.sh' >> ~/.bashrc
     # source .bashrc or restart shell
 
 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]
+    [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. 
+`otconfig` is the only command not taking an argument, it sets the environment variables for all services. 
 
-Start all services with:
+Start all services and the 4store backend with:
 
     otstart all 
 
-Kill all services with:
+Kill all services and the 4store backend with:
     
     otkill all
 
@@ -80,30 +125,34 @@ It is possible to manage single services (e.g. `otstart dataset` to run dataset
 
 # Access web services
 
-The default port setting (see default config file ~/.opentox/config/default.rb):
+The default port setting for the web services and the 4store backend,  (see config files `~/.opentox/config/*.rb`):
 
-    Algorithm: localhost:8081/algorithm
-    Compound: localhost:8082/compound
-    Dataset: localhost:8083/dataset
-    Feature: localhost:8084/feature
-    Model: localhost:8085/model
-    Task: localhost:8086/task
-    Validation: localhost:8087/validation
-    4store: localhost:8088/
+| Service | URI | 
+| ------ | ------ |
+| --------------------  | ------------------------------------- |
+| Algorithm | localhost:8081/algorithm | 
+| Compound | localhost:8082/compound |
+| Dataset | localhost:8083/dataset |
+| Feature | localhost:8084/feature |
+| Model | localhost:8085/model |
+| Task | localhost:8086/task |
+| Validation | localhost:8087/validation |
+| 4store | localhost:9088/ |
 
-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. 
+NOTE: Only installed service URIs are set in the config files. Model and validation service are not available yet. 
 
 # Testing services
 
-    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
+    ruby test/dataset-large.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 $OT_PREFIX/opentox-test/test.
+The tests take some time and finish with a short report:
+
+    Finished tests in 43.827407s, 0.9811 tests/s, 4.4265 assertions/s.
+    42 tests, 194 assertions, 2 failures, 0 errors, 0 skips
+
+To test one specific service, run its script (`ruby [service_name].rb`) located in `$OT_PREFIX/opentox-test/test`.
 
diff --git a/_posts/2012-08-20-how-to-grant-gemcutter-perimssions.md b/_posts/2012-08-20-how-to-grant-gemcutter-perimssions.md
new file mode 100644
index 0000000..ef951ee
--- /dev/null
+++ b/_posts/2012-08-20-how-to-grant-gemcutter-perimssions.md
@@ -0,0 +1,12 @@
+---
+layout: post
+title: "How to grant gemcutter perimssions"
+description: ""
+category: general
+tags: [development]
+---
+{% include JB/setup %}
+
+Grant gemcutter push permissions by creating another owner:
+
+    gem owner -a EMAIL GEM_NAME
diff --git a/_posts/2012-08-23-install-production-webservice-gems.md b/_posts/2012-08-23-install-production-webservice-gems.md
new file mode 100644
index 0000000..890184f
--- /dev/null
+++ b/_posts/2012-08-23-install-production-webservice-gems.md
@@ -0,0 +1,16 @@
+---
+layout: post
+title: "Install production webservice gems"
+description: ""
+category: general
+tags: [installation, gem]
+---
+{% include JB/setup %}
+The installation of opentox-webservices is straightforward with the `gem` command, e.g.
+
+    gem install opentox-dataset 
+    gem install toxbank-investigation
+
+This will install the webservice and all dependencies in your gem path.
+Please do not forget to configure the webservice in `~/.opentox/config/<webservice>.rb`.
+In some cases (eg. compound and algorithm) large external libraries have to be compiled - please be patient.