Hi folks, Could anybody answer my question and help me figure it out? Thank you so much! Best, Xiaofei ________________________________ From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Wang, Xiaofei [xfwang@ku.edu] Sent: Thursday, March 06, 2014 4:41 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) 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