Question: galaxy tool dependency
gravatar for jaganlakshman
4.6 years ago by
United States
jaganlakshman10 wrote:

Can anyone help me with the following step in Galaxy local tools install. In fact i could able to install tools from tool shed but all installed tools says missing dependency and set dependency in universe.wsgi.ini. i just created folder called dependency_dir and used its path pasted against  tool_dependency_dir = dependency_dir in universe.wsgi.ini. And restarted galaxy. but still couldn't run programs. I new to computational analysis and was bench scientist all along. appreciate the galaxy forum for helping me so far. i tried the galaxy server but couldn't wait for the queue. 

2. Set directory for tool dependencies

You should set a path to existing directory where Galaxy will store tool dependencies. You should do that by uncomenting and setting valuetool_dependency_dir in the Galaxy config file universe.wsgi.ini.

You can create directory named path/to/galaxy/dependency_dir and the line in Galaxy config will look like this:

tool_dependency_dir = dependency_dir

Restart Galaxy after you modify the config file for changes to take effect.

galaxy • 3.5k views
ADD COMMENTlink modified 4.6 years ago by Greg Von Kuster810 • written 4.6 years ago by jaganlakshman10

How exactly does the line starting with tool_dependency_dir look like in your universe.wsgi.ini?

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Martin Čech ♦♦ 4.9k
gravatar for Greg Von Kuster
4.6 years ago by
Penn State University
Greg Von Kuster810 wrote:

Hello, based on your comments, you may have installed the repositories before you had set your tool_dependency_dir.  If this is the case, then each repository that defines a tool dependency will show the tool dependency in a Never installed state.  You can either:

-uninstall and reinstall all of the repositories.  You can do this on the Manage installed tool shed repositories page from the admin view


-for each repository that has a tool dependency in the Never installed state, you can elect to install the tool dependency.  You can do this by selecting the repository from the Manage installed tool shed repositories from the Admin view, then from the repository Actions popup menu in the upper right corner, Manage tool dependencies.


Greg Von Kuster


ADD COMMENTlink written 4.6 years ago by Greg Von Kuster810

Greg also implemented a "repair repository" feature that is very useful. Navigate to your repository that is on top of your dependency hierarchy and select "repair repository". The entire dependency tree will be traversed and repaired.


ADD REPLYlink written 4.6 years ago by Bjoern Gruening5.1k
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