Re: [galaxy-dev] Problem installing tool_ Galaxy local
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 NameDescription Owner RevisionStatus 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" To: "Valeria Parreira Pinto" Cc: "galaxy-...@bx.psu.edu Dev" 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: 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
Re: [galaxy-dev] Problem installing tool_ Galaxy local
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" To: "Valeria Parreira Pinto" Cc: "galaxy-...@bx.psu.edu Dev" 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_
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 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 RevisionStatus > s_martS-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" > To: "Valeria Parreira Pinto" > Cc: "galaxy-...@bx.psu.edu Dev" > 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 > 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" > To: "Valeria Parreira Pinto" > Cc: "galaxy-...@bx.psu.edu Dev" > 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 > 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
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 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" > To: "Valeria Parreira Pinto" > Cc: "galaxy-...@bx.psu.edu Dev" > 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 > 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_updat
Re: [galaxy-dev] Problem installing tool_ Galaxy local
> 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" > To: "Valeria Parreira Pinto" > 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 > 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 > > ___ > 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/
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 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 > > ___ > 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/
