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!
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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