Hi Valeria, On Dec 5, 2013, at 4:59 PM, Valeria Parreira Pinto <vparreir@uoguelph.ca> wrote:

Hi Greg, I have done that...take a look. However this time I saw something different see below

Installed tool shed repositories Update tool shed status

Advanced Search

You can now attempt to install the repository named s_mart again.

Name ↓ Description Owner Revision Installation Status Tool shed

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 New toolshed.g2.bx.psu.edu Updates are available in the Tool Shed for this revision A newer installable revision is available for this repository This is the latest installable revision of this repository This repository is deprecated in the Tool Shed This repository contains exported workflows Unable to get information from the Tool Shed

The above page showing that the s_mart repository is in the New state implies that it is ready for installation, You can install it by clicking the right part of the s_mart button which will pop up a menu from which you can choose to install the repository. After the repository goes through the installation process, it should be displayed in the Installed state. If there were errors, it wil be in an Error state. If it si in an Installed state with no errors, then you should be able to see any contained tools in your Galaxy tool panel.

and then this time I could see S-MART in the list:

NGS: Mapping NGS: Indel Analysis NGS: RNA Analysis NGS: SAM Tools NGS: GATK Tools (beta) NGS: Peak Calling NGS: Simulation Phenotype Association VCF Tools S-MART Choose an existing section in your tool panel to contain the installed tools (optional).

Clicking Install without selecting a tool panel section will load the installed tools into the tool panel outside of any sections.

It did not work and I can not see S-MART in my tool box. Thank you for your attention. VP ___________________________________________

From: "Greg Von Kuster" <greg@bx.psu.edu> To: "Valeria Parreira Pinto" <vparreir@uoguelph.ca> Cc: "galaxy-dev@bx.psu.edu Dev" <galaxy-dev@bx.psu.edu> Sent: Thursday, December 5, 2013 4:33:34 PM Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local

Click on the "Admin" option from the top menu bar, then click on the "Mange installed tool shed repositories. The find the "s_mart" repository from that page and clck on it. The from the "Repository Actions" menu, select "Reset to install" or "Repair repository" if it is available.

On Dec 5, 2013, at 4:08 PM, Valeria Parreira Pinto <vparreir@uoguelph.ca> wrote:

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

From: "Greg Von Kuster" <greg@bx.psu.edu> To: "Valeria Parreira Pinto" <vparreir@uoguelph.ca> Cc: "galaxy-dev@bx.psu.edu Dev" <galaxy-dev@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 <vparreir@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" <greg@bx.psu.edu> To: "Valeria Parreira Pinto" <vparreir@uoguelph.ca> Cc: "galaxy-dev@bx.psu.edu Dev" <galaxy-dev@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 <vparreir@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" <greg@bx.psu.edu> To: "Valeria Parreira Pinto" <vparreir@uoguelph.ca> Cc: galaxy-dev@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 <vparreir@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

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