Installation instruction

Getting Started

ChemicalToolBoX can be installed on all common unix systems. However, it is developed on Linux and I don't have access to OS X. You are welcome to help improving this documentation, just contact me.

Prerequisites:

* Python 2.6 or above
* standard C compiler, C++ and Fortran compiler
* Autotools
* CMake
* cairo development files (used for PNG depictions)
* python development files
* Java Runtime Environment (JRE, used by OPSIN and NPLS)

• Debian based systems: apt-get install build-essential gfortran cmake mercurial libcairo2-dev python-dev
• Fedora: yum install make automake gcc gcc-c++ gcc-gfortran cmake mercurial libcairo2-devel python-devel
• OS X (MacPorts): port install gcc cmake automake mercurial cairo-devel

1. Clone the latest Galaxy platform:

   hg clone https://https://bitbucket.org/galaxy/galaxy-central/
   

2. Navigate to the galaxy-central folder and update it:

   cd ~/galaxy-central
   hg pull
   hg update
   

3. Create folders for toolshed and dependencies:

   mkdir ~/shed_tools
   mkdir ~/galaxy-central/tool_deps
   

4. Create configuration file:

   cp ~/galaxy-central/universe_wsgi.ini.sample ~/galaxy-central/universe_wsgi.ini
   

5. Open universe_wsgi.ini and change the dependencies directory:

   LINUX: gedit ~/galaxy-central/universe_wsgi.ini
   OS X: open -a TextEdit ~/galaxy-central/universe_wsgi.ini
   

6. Search for tool_dependency_dir = None and change it to tool_dependency_dir = ./tool_deps

7. Remove the hash in front of tool_config_file and tool_path

8. (Re-)Start the galaxy daemon:

   GALAXY_RUN_ALL=1 sh run.sh --stop-daemon
   GALAXY_RUN_ALL=1 sh run.sh --daemon
   

After launching galaxy is accessible via the browser at http://localhost:8080/.

To improve the overall performance of NumPy you need to disable CPU throttling:

cpufreq-selector -g performance

Admin Account

• Register a new account

• Promote user to admin

  • open universe_wsgi.ini
  • search admin_users = None and change it to admin_users = YOUR_EMAIL_ADDRESS

Toolshed

Installation via webbrowser

• go to the admin page
• select Search and browse tool sheds
• Galaxy test tool shed > Computational chemistry > chemicaltoolbox
• install chemicaltoolbox

API Installation

• Generate an API Key

• Run the installation script:

  python ./scripts/api/install_tool_shed_repositories.py --api YOUR_API_KEY
  -l http://localhost:8080 --url http://testtoolshed.g2.bx.psu.edu/ -o bgruening
  -r 2c9d1a52824d --name chemicaltoolbox --tool-deps --repository-deps
  --panel-section-name ChemicalToolBoX
  

JMol Editor Installation

JMol Editor needs be run on a webserver, this is how to setup the server:

• copy the directory jmoleditor from /galaxytools/chemicaltoolbox/data_source/ into your Galaxy Root directory

  cp -a ~/galaxytools/chemicaltoolbox/data_source/jmoleditor/ ~/galaxy-central/
  

• launch the webserver

  python -m SimpleHTTPServer &