Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! ________________________________ From: Greg Von Kuster [greg@bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) 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" <xfwang@ku.edu<mailto:xfwang@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/<http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies>Tool<http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies>%20Dependencies<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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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