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---
layout: post
title: "Install opentox development environment"
description: ""
category: Installation
tags: [Deployment, Ubuntu, Debian, Setup]
---
{% include JB/setup %}
Architecture overview and how to install recent opentox services on Ubuntu or Debian.
# Philosophy
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 the 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 (ot-tools) is available.
4. To uninstall, simply remove the line from the startup file. To save disc space also remove directory `OT_PREFIX` (not recommended). To remove also the configuration, remove `~/.opentox` (not recommended).
<br>
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<hr>
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# Installation
Installation (`development` at the point of writing this = 08/2012) tested with Debian 6.0.5 and Ubuntu 11.04. Installer available at [github](https://github.com/opentox/install).
Check you can run "sudo" commands (e.g. `sudo ls`), which is required for base packages. Install git:
# Install git
sudo apt-get install git
Add your public key at `https://github.com`. 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 with your favorite editor
./install silent
This will prepare the system for opentox web services, including dependencies.
# Install OpenTox services
Load environment (general):
. $HOME/.opentox/config/install/config.sh
. $OT_PREFIX/install/utils.sh
Load environment (with BASH):
. $HOME/.opentox/ot-tools.sh
otconfig
Download and install opentox-client and opentox-server:
for f in opentox-client opentox-server; do
git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
cd $OT_PREFIX/$f
git checkout development 2>/dev/null
done
cd $OT_PREFIX/opentox-client/bin
./opentox-client-install silent
cd $OT_PREFIX/opentox-server/bin
./opentox-server-install silent
Download and install services and tests:
for f in algorithm compound dataset feature model validation task opentox-test; do
git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f
cd $OT_PREFIX/$f
git checkout development 2>/dev/null
if [ -f $OT_PREFIX/$f/bin/$f-install ]; then
cd $OT_PREFIX/$f/bin
./$f-install silent
fi
done
notify
OpenTox compatible web services are now installed and configured.
# Activate and use ot-tools for BASH
NOTE: ot-tools require BASH.
Add ot-tools to your `.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]
`otconfig` is the only command not taking an argument. It sets the environment variables for all services.
Start all services and the 4store backend with:
otstart all
Kill all services and the 4store backend 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 for the web services and the 4store backend, (see config files `~/.opentox/config/*.rb`):
| 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.
# Testing services
cd $OT_PREFIX/opentox-test
otconfig
ruby opentox-client.rb
ruby test/dataset-large.rb
The tests take some time and finish with a short report:
Finished tests in 44.690815s, 0.9622 tests/s, 4.4528 assertions/s.
43 tests, 199 assertions, 1 failures, 0 errors, 0 skips
To test one specific service, run its script (`ruby [service_name].rb`) in `$OT_PREFIX/opentox-test/test`.
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