Hi Valeria, Please always replay-all to keep email threads on the original list.
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 On Dec 5, 2013, at 12:13 PM, Valeria Parreira Pinto <vparr...@uoguelph.ca> wrote: > Hi Greg, > > Unfortunately, it is not working...sorry bug you again. > I know nothing about programming...this is what I have done: ( I have tried > to follow http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies) > > In universe_wsgi.ini modified > #tool_dependency_dir = None > tool_dependency_dir = tool_dependencies > > In shell > > Valerias-MacBook-Pro:galaxy-dist vrparreira$ cd tool_dependencies > Valerias-MacBook-Pro:tool_dependencies vrparreira$ mkdir smart > Valerias-MacBook-Pro:tool_dependencies vrparreira$ cd > Valerias-MacBook-Pro:~ vrparreira$ cd galaxy-dist > Valerias-MacBook-Pro:galaxy-dist vrparreira$ sh run.sh --reload > > > This is what I see on the shell (I am not sure that is necessary): > > 127.0.0.1 - - [05/Dec/2013:11:52:59 -0400] "GET > /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=613e73b56070623c&changeset_revisions=b6481845eb0d > HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/browse_repositories?status=done&message=You+can+now+attempt+to+install+the+repository+named+%3Cb%3Es_mart%3C%2Fb%3E+again."; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/31.0.1650.63 Safari/537.36" > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,026 Loading new tool panel > section: S-MART > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:53:16,026 Adding new row > (or updating an existing row) for repository 's_mart' in the > tool_shed_repository table, status set to 'New'. > tool_shed.util.tool_util DEBUG 2013-12-05 11:53:16,039 Appending to tool > panel section: S-MART > 127.0.0.1 - - [05/Dec/2013:11:53:15 -0400] "POST > /admin_toolshed/prepare_for_install HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=613e73b56070623c&changeset_revisions=b6481845eb0d"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:19 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:22 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:25 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:28 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:31 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:34 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:37 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:40 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:43 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:46 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:49 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:52 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:55 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:53:58 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > tool_shed.util.shed_util_common DEBUG 2013-12-05 11:54:00,240 Error cloning > repository: case-folding collision between > SMART/Java/Python/compareOverlapping.py and > SMART/Java/Python/CompareOverlapping.py > tool_shed.galaxy_install.repository_util DEBUG 2013-12-05 11:54:00,624 > Removed repository installation directory: > /Users/vrparreira/shed_tools/toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/b6481845eb0d > 127.0.0.1 - - [05/Dec/2013:11:53:16 -0400] "POST > /admin_toolshed/manage_repositories HTTP/1.1" 302 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:00 -0400] "GET > /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e > HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/prepare_for_install"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:01 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:04 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:07 -0400] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:08 -0400] "GET > /admin_toolshed/manage_repository?id=f2db41e1fa331b3e HTTP/1.1" 200 - > "http://localhost:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:17 -0400] "GET > /admin_toolshed/browse_repositories HTTP/1.1" 200 - > "http://localhost:8080/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:23 -0400] "GET > /admin/review_tool_migration_stages HTTP/1.1" 200 - > "http://localhost:8080/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:35 -0400] "GET > /admin_toolshed/monitor_repository_installation?tool_shed_repository_ids=f2db41e1fa331b3e > HTTP/1.1" 200 - "http://localhost:8080/admin"; "Mozilla/5.0 (Macintosh; Intel > Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 > Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:44 -0400] "GET /admin/reload_tool HTTP/1.1" > 200 - "http://localhost:8080/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X > 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 > Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:51 -0400] "GET > /forms/browse_form_definitions HTTP/1.1" 200 - "http://localhost:8080/admin"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/31.0.1650.63 Safari/537.36" > 127.0.0.1 - - [05/Dec/2013:11:54:54 -0400] "GET > /admin_toolshed/browse_repositories HTTP/1.1" 200 - > "http://localhost:8080/admin"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) > AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" > > > If you could help me it would be great. Thanks in advance, > Valeria > _____________________________________________ > Valeria Parreira, Ph.D > Adjunct Faculty > Department of Pathobiology > OVC, University of Guelph, > Guelph, Ontario, N1G 2W1, Canada > Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) > vparr...@uoguelph.ca > > From: "Greg Von Kuster" <g...@bx.psu.edu> > To: "Valeria Parreira Pinto" <vparr...@uoguelph.ca> > Cc: galaxy-...@bx.psu.edu > Sent: Wednesday, December 4, 2013 3:54:26 PM > Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local > > Hello Valeria, > > The setting for tool_dependency_dir must be an actual path on your local file > system, something like: > > tool_dependency_dir = ../tool_dependencies > > Make sure that you set the location to a place that is safe for installing > files. > > Greg Von Kuster > > On Dec 4, 2013, at 3:09 PM, Valeria Parreira Pinto <vparr...@uoguelph.ca> > wrote: > > Hi > > I am having problems to install a tool from tool shed named S_MART (attached > paper) on my local Galaxy. > The reason to install S_MART is to use DETR'PROK (attached paper) in Galaxy. > The first time, I got a warning before installing S-MART saying: > " set the value of your tool_dependency_dir setting in universe_wsgi_ini and > restart before installing" > > In the universe_wsgi_ini: > > 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_dependency_dir > > I have follow the instructions of the Matthias Zytnicki (paper's author). I > did not work, still with error, however now it does not mention where or what > to do!! > > Could you please let me know what would be the problem? and How to fix it? > Thanks in advance, > Valeria > > > _____________________________________________ > Valeria Parreira, Ph.D > Adjunct Faculty > Department of Pathobiology > OVC, University of Guelph, > Guelph, Ontario, N1G 2W1, Canada > Tel: +1 (519) 824-4120 - Ext. 54717(lab) and 54679 (office) > vparr...@uoguelph.ca > > <DETR_PROK.pdf><SMART.pdf>___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
