galaxy_notes

CHANGE USER TO ADMIN
       Go to the galaxy-dist/universe_wsgi.ini
       Find the line that starts with 'admin_users = '
       Add your user / e-mail address
       Uncomment the line
       Restart GALAXY

INSTALL A TOOL FROM THE TOOL-SHED
	Go to the galaxy-dist/universe_wsgi.ini
	Find the line that starts with 'tool_config_file ="
	Uncomment the line
	Restart GALAXY
	---
	In GALAXY, Go to Admin->Search and browse tool sheds
	Select Galaxy main tool shed->Browse valid repositories
	Find the tool you're interested in->Preview and install
	Click 'Install to Galaxy' in the top right corner
	---
	In the 'universe_wsgi.ini' file, set the 'tool_dependency_dir'
	to the directory galaxy-dist/tool-dependency-dir/
	Make that directory
	Restart GALAXY
	---
	After installation, the tools .xml file will be in the
	../shed_tools/ directory and the tools' dependencies in the
	tool-dependency-dir/ directory

ADDING A NEW TOOL SECTION
       After adding a new tool from the Tool Shed, 
       and in addition adding a new section,
       this section will be added to the 'shed_tool_conf.xml' file.
       So I think, depending on the source of the sections content tools,
       they are added to different 'conf.xml' files
 

THE universe_wsgi.ini FILE.
    Any change in this file comes into effect after restarting GALAXY

GENERAL INFORMATION
	The 'Tools' list in GALAXY on the left have a corresponding
	.xml file, the 'tool_conf.xml' file

EDIT A WORKFLOW
       In the workflow design you don't specify the input and output yet.
       You do that when you want to run the workflow.