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:
#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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