What happens if you choose "Reset to install" from the "Repository Actions" 
menu?  You should be presented with a page that shows the repository as 
uninstalled, at which time you can attempt to install it again.


On Dec 5, 2013, at 3:11 PM, Valeria Parreira Pinto <vparr...@uoguelph.ca> wrote:

> Hi Greg,
> 
> It did not work...This is what I see:
> 
> 
> This repository is not installed correctly (see the Repository installation 
> error below). Choose Reset to install from the Repository Actions menu, 
> correct problems if necessary and try installing the repository again.
> 
> However, there no information regarding ti the error below.
> What is your suggestion?
> VP
> 
> 
> 
> 
> From: "Greg Von Kuster" <g...@bx.psu.edu>
> To: "Valeria Parreira Pinto" <vparr...@uoguelph.ca>
> Cc: "galaxy-...@bx.psu.edu Dev" <galaxy-...@bx.psu.edu>
> Sent: Thursday, December 5, 2013 1:19:59 PM
> Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local
> 
> 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
> _____________________________________________
> 
> 
> 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
> 
> 
> 
> 
> <DETR_PROK.pdf><SMART.pdf>___________________________________________________________
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