Hi Greg, 

I have done at least twice just to double check From Repository actions - reset 
to install 
This is what a I see: 





Monitor installing tool shed repositories 
Name    Description     Owner   Revision        Status 
s_mart  S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many 
different plots to visualize your data.    yufei-luo       b6481845eb0d    

Error 







The page Monitor installing tool shed repositories.... status error... 
VP 









----- Original Message -----

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 3:45:04 PM 
Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local 

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 






----- Original Message -----

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: 



<blockquote>


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: 

<blockquote>


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 



_____________________________________________ 


----- Original Message -----

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: 

<blockquote>



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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</blockquote>

</blockquote>

</blockquote>


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