Re: [galaxy-dev] Problem installing tool_ Galaxy local
Hello Valeria, Unfortunately the s_mart repository seems to be in a broken state on the main Galaxy Tool Shed. I assume you are installing the repository from the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/yufei-luo/s_mart Some of the tools (maybe all, I haven't looked at all of them) define functional tests, but the repository does not contain any of the test data files, so the Tool Shed's install and test framework cannot validate the tools in this repository. You'll notice that the repository's "Automated tool test results" container displays this: Automated tool test results Tool test results Automated test environment Tools missing tests or test data The error I get installing s_mart from the main Tool Shed is the following. I believe this error may be osx specific. Are you trying to install into an osx environment? If not, can you send the snippet of your Galaxy paster log so we can see the error you are encountering? Error cloning repository: case-folding collision between SMART/Java/Python/compareOverlapping.py and SMART/Java/Python/CompareOverlapping.py Fixing the above problem requires the repository owner, so you'll have to contact them and let them know of the problem. You can contact the owner via the Repository Actions popup menu for the repository. If you contact them, perhaps you can also let them know they should add functional test data for the tests defined in the repository's tools. Thanks, Greg Von Kuster On Dec 5, 2013, at 8:50 PM, Valeria Parreira Pinto <vparreir@uoguelph.ca> wrote:
Hi Greg, Sorry if I lost you sending you the wrong screen. I have done all those steps, I saw that screen, than I clicked smart button, it went to another screen (which asks the name of the new tool and where to place) (which I sent part of it, showing the smart icon) for installation. Next step, I could see the status as cloning (yellow) and then error (red ). I have done at least 3 times...always shows status:error VP
_____________________________________________ 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) vparreir@uoguelph.ca
----- Original Message ----- 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: Thu, 05 Dec 2013 19:32:22 -0500 (EST) Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local
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&chang... HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories?status=done&mes...." "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:..." "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 > > > > > <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/
Hi Greg, Thank you very much for your attention. You are right, I am installing from the main Tool Shed ( http://toolshed.g2.bx.psu.edu/view/yufei-luo/s_mart), and in a OSX enviroment (MacPro). I have already contact the owner describing the problems and your suggestions...let's see. Have a nice weekend, VP ----- Original Message ----- 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: Friday, December 6, 2013 9:51:17 AM Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local Hello Valeria, Unfortunately the s_mart repository seems to be in a broken state on the main Galaxy Tool Shed. I assume you are installing the repository from the main Tool Shed: http://toolshed.g2.bx.psu.edu/view/yufei-luo/s_mart Some of the tools (maybe all, I haven't looked at all of them) define functional tests, but the repository does not contain any of the test data files, so the Tool Shed's install and test framework cannot validate the tools in this repository. You'll notice that the repository's "Automated tool test results" container displays this: Automated tool test results Tool test results Automated test environment Tools missing tests or test data The error I get installing s_mart from the main Tool Shed is the following. I believe this error may be osx specific. Are you trying to install into an osx environment? If not, can you send the snippet of your Galaxy paster log so we can see the error you are encountering? Error cloning repository: case-folding collision between SMART/Java/Python/compareOverlapping.py and SMART/Java/Python/CompareOverlapping.py Fixing the above problem requires the repository owner, so you'll have to contact them and let them know of the problem. You can contact the owner via the Repository Actions popup menu for the repository. If you contact them, perhaps you can also let them know they should add functional test data for the tests defined in the repository's tools. Thanks, Greg Von Kuster On Dec 5, 2013, at 8:50 PM, Valeria Parreira Pinto < vparreir@uoguelph.ca > wrote: Hi Greg, Sorry if I lost you sending you the wrong screen. I have done all those steps, I saw that screen, than I clicked smart button, it went to another screen (which asks the name of the new tool and where to place) (which I sent part of it, showing the smart icon) for installation. Next step, I could see the status as cloning (yellow) and then error (red ). I have done at least 3 times...always shows status:error VP _____________________________________________ 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) vparreir@uoguelph.ca ----- Original Message ----- 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: Thu, 05 Dec 2013 19:32:22 -0500 (EST) Subject: Re: [galaxy-dev] Problem installing tool_ Galaxy local 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&chang... HTTP/1.1" 200 - "http://localhost:8080/admin_toolshed/browse_repositories?status=done&mes...." "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:..." "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 > > > > > <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/
participants (2)
-
Greg Von Kuster -
Valeria Parreira Pinto