Hello Ted, Please replay-all to back-and-forth communication like this so that the thread stays on the mailing list. You can also search the Galaxy mailing lists for answers to your questions - see http://galaxy.psu.edu/search/mailinglists/.
See my answers below. On Dec 28, 2011, at 11:46 PM, Ted Goldstein wrote: > Greg, > Thanks. I reinstalled from galaxy-centlral and it works fine. I'd rather be > on the dev branch. > > Two other topics: > 1. I would like to take a crack at > https://bitbucket.org/galaxy/galaxy-central/issue/554/show-column-names-headers-or-first-entry > Can you give me a clue about which files to work on? I haven't been working in this area for quite some time, and have not been involved in the discussion on the mail thread and bitbucket ticket for this, so I'm not the best person to answer your questions. That being said, if I understand the issue correctly, I would start by looking at the ColumnListParameter() class in ~/lib/galaxy/tools/parameters/basic.py. > > > 2. When I hit control-c, the server process stops answering but doesn't > terminate. Is this correct? See this thread (there are others as well if you search the mailing list archives with various search strings): http://galaxy-users-list-archive.2308625.n4.nabble.com/restart-server-td4131372.html > > Thanks! > Ted > > On Dec 28, 2011, at 5:30 AM, Greg Von Kuster wrote: > >> Hello Ted, >> >> I assume you cloned your local Galaxy instance from our distribution repo at >> https://bitbucket.org/galaxy/galaxy-dist. >> >> Unfortunately, in order to make use of the features that enable >> communication between your local Galaxy instance and a Galaxy tool shed, you >> have to update your local Galaxy instance from our Galaxy central repo at >> https://bitbucket.org/galaxy/galaxy-central. This is because the >> distribution repo is not updated as often as is necessary to keep current >> with the rapidly evolving tool shed code base and feature set. This issue >> should be eliminated at some point. >> >> >> On Dec 27, 2011, at 11:54 PM, Ted Goldstein wrote: >> >>> Hello, >>> I just installed Galaxy and am very impressed. But I am having problems >>> adding in tools from the toolshed. When I click on adding a tool such as >>> the Venn Diagram tool, it brings up the following message (even though I >>> never installed it before: >>> >>> ============ >>> Found >>> >>> The resource was found at >>> xyzzy.ucsc.edu:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=9956e395db5a106ba074ae610c525fa17cec3b14:7b2276656e6e5f6c697374223a205b22447261772056656e6e204469616772616d2028504446292066726f6d206c69737473222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f70657465726a632f76656e6e5f6c697374222c2022626166373033316434373065225d7d&includes_tools=True; >>> you should be redirected automatically. >>> WSGI Server >>> ================= >>> >>> >>> The page never redirects. As well the URL is malformed (missing the >>> "http:"). If I fabricate this by hand. E.g. >>> http://xyzzy.ucsc.edu:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=9956e395db5a106ba074ae610c525fa17cec3b14:7b2276656e6e5f6c697374223a205b22447261772056656e6e204469616772616d2028504446292066726f6d206c69737473222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f70657465726a632f76656e6e5f6c697374222c2022626166373033316434373065225d7d&includes_tools=True >>> >>> ============ >>> Not Found >>> >>> The resource could not be found. >>> No route for /admin_toolshed/install_repository >>> ============ >>> The log file shows: >>> .2.3.4 - - [27/Dec/2011:20:33:27 -0700] "GET /admin/browse_tool_sheds >>> HTTP/1.1" 200 - "http://xyzzy.ucsc.edu:1234/admin"; "Mozilla/5.0 (Macintosh; >>> U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25) Gecko/20111212 Firefox/3.6.25" >>> 1.2.3.4 - - [27/Dec/2011:20:33:30 -0700] "GET >>> /admin/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F >>> HTTP/1.1" 302 - "http://xyzzy.ucsc.edu:1234/admin/browse_tool_sheds"; >>> "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25) >>> Gecko/20111212 Firefox/3.6.25" >>> 1.2.3.4 - - [27/Dec/2011:20:44:28 -0700] "GET >>> /admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=9956e395db5a106ba074ae610c525fa17cec3b14:7b2276656e6e5f6c697374223a205b22447261772056656e6e204469616772616d2028504446292066726f6d206c69737473222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f70657465726a632f76656e6e5f6c697374222c2022626166373033316434373065225d7d&includes_tools=True >>> HTTP/1.1" 404 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; >>> en-US; rv:1.9.2.25) Gecko/20111212 Firefox/3.6.25" >>> >>> =============== >>> >>> I looked through the mailing list and wiki and I don't see this problem. >>> Could I have misinstalled or misconfigured something? >>> >>> Thanks for the great system! >>> >>> Best regards, >>> Ted >>> >>> >>> Ted Goldstein >>> t...@soe.ucsc.edu >>> Ph.D. Candidate, HausslerLab, CBSE, UCSC >>> (650) 743-4141 >>> http://soe.ucsc.edu/~ted >>> >>> >>> ___________________________________________________________ >>> 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/ >> >> Greg Von Kuster >> Galaxy Development Team >> g...@bx.psu.edu >> >> >> > > Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___________________________________________________________ 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/
