Hello,

It's difficult to determine the cause of the problem in your environment based 
on the details you've provided.  If you have defined your tool_dependeny_dir 
configuration setting in your universe_wsgi.ini to be ../tool_dependencies, 
then the tool shed installation process will install tool dependencies there.  
If you see them installed elsewhere, then that setting must have been set 
differently at the time they were installed.  You can try setting it to the 
location where your tool dependencies have been installed (i.e., the Galaxy 
installation directory), restat your server and uninstall them.  Then you can 
reset it to the more appropriate location (e.g., ../tool_dependencies), restart 
yiour server and reinstall them.  If you have tool dependencies installed in 
multiple locations, you'll have to be careful to use a process that will 
eventually result in all tool dependencies installed into a single location.

Greg Von Kuster


On Mar 6, 2014, at 5:41 PM, "Wang, Xiaofei" <xfw...@ku.edu> wrote:

> Dear there,
> 
> I am trying to install some tools from toolshed on my local galaxy instance, 
> like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and 
> sam_to_bam. For the first time, I got a warning before installing, something 
> like this " set the value of your tool_dependency_dir setting in 
> universe_wsgi_ini and restart before installing".
> 
> Then, I followed the answer on this thread (Problem installing tool_ Galaxy 
> local) as below. I edited the universe_wsgi_ini like this:
> 
> #Path to the directory in which managed tool dependencies are placed.  To use
> # the dependency system, see the documentation at:
> # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
> #tool_dependency_dir = None 
> tool_dependency_dir = ../tool_dependencies  
> 
> Then, I restarted and installed the tool again. Galaxy create a directory 
> named tool_dependencies at the same level in local file system hierarchy as 
> the galaxy installation directory (same level as galaxy-dist). Some softwares 
> such as bwa and picard are installed automatically here. But, when I checked 
> in the admin "manage installed tool shed repositories", the installation 
> status is "Installed, missing tool dependencies" for the four tools I 
> mentioned above. I do not know why this happened in my case? I tried to 
> figure it out follow this thread "The migrated BWA installed but missing 
> dependencies". But, I did not get the idea. 
> 
> Could you tell me why this happen and how to fix it up?
> 
> Thank you so much!
> 
> ------------------------------------------------------------------------------------------
> Your setting for tool_dependency_dir should not be as you've stated:
> 
>> tool_dependency_dir = tool_dependencies
> 
> 
> It should be an actual path on your local file system, something like:
> 
> tool_dependency_dir = ../tool_dependencies
> 
> If you use the above setting, then Galaxy should create a directory named 
> tool_dependency_dir at the same level in your local file system hierarchy as 
> your Galaxy installation directory.
> 
> I cannot guarantee that this change will solve your problem, but it will be a 
> step in the right direction.  After making this change, let us know if you 
> still see problems.
> 
> Greg Von Kuster
> 
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