Importing a tool shed in your own Galaxy

Tools in Galaxy are stored in a tool shed. As you might have noticed in the RNA-Seq training, the BITS Galaxy tool shed contains tools that you cannot find in the main Galaxy. Fortunately, you can obtain these tools from our tool shed and store them on your local Galaxy server.

The easiest way to import tools from other tool sheds is to import the entire tool shed in your Galaxy. We will give the example here of importing the Genouest tool shed. You can import the BITS tool shed in exactly the same way.

• Log on as administrator to your Galaxy server
• Change to the galaxy user:

  su galaxy

• Go to the home directory of the galaxy user:

  cd

• Go to the Galaxy base folder (the folder that contains all configuration files, the tools folder... ask your system administrator for its location)
• Open the file called tool_sheds_conf.xml:

  nano tool_sheds_conf.xml

• Add the following line of text: <tool_shed_name="Genouest tool shed" url=http://toolshed.genouest.org/"/> as shown in the figure below:
  
  
  

  Of course if you are importing the BITS tool shed you add the following line: <tool_shed_name="BITS tool shed" url=http://toolshed.bits.vib.be"/>

• Close and save the file (Ctrl+X in nano)
• Restart the Galaxy server:

  service galaxyd restart

Now the tool shed should have been added to your Galaxy.

• Go to the webpage of your Galaxy
• Login as administrator
• Click Admin in the top menu
  
  
  
• In the left menu go to the Tool sheds section and click Search and browse tool sheds
  
  
  

The tool shed that you have added should be included in the list of tool sheds. You can now install tools from the newly imported tool shed.