On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | <joachim.ja...@vib.be> wrote: > Hi Greg, > > > Sorry to dig up this unsolved thread from a few months back. > > Recap of the bug: I have developed a small tool. I have put it in my local > Toolshed, and installed it. After applying some changes to the tool, I 'hg > push'ed the changes to my repository on my toolshed. I uninstalled the tool, > and reinstalled it. Since I work with job handlers, I have to restart > Galaxy. Since I had about ~4 committed changes, I have repeated these steps > about 4 times. > > The bug: the tool appears multiple times in the tool management window. 2 > times as new, and 1 time as uninstalled (since I uninstalled it). The tool > is still available in the toolbox, although it should not. The 2 installed > tools have an option 'install', but when I click this I get an internal > server error 500. > > Galaxy version: > ************* > [galaxy@galaxy galaxy-dist]$ hg tip > changeset: 10411:c42567f43aa7 > tag: tip > user: greg > date: Mon Aug 19 13:19:56 2013 -0400 > summary: Filter invalid objects when generating the list of > repository_dependencies objects that are associated with a tool shed > repository installed into Galaxy. > ************* > > As per your request: the web log of this internal server error. > > **************** > 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] "GET > /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/&repository_ids=968205d9ed31733d&changeset_revisions=e08a6d9e97a3 > HTTP/1.1" 500 - > "http://galaxy.bits.vib.be/admin_toolshed/browse_repositories"; "Mozilla/5.0 > (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu > Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36" > Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486 > **************** > > The postgres database shows: > > ************************ > galaxydb=> select id, tool_shed, name, owner, > installed_changeset_revision, status, error_message from > tool_shed_repository where name = 'transpose'; > id | tool_shed | name | owner | > installed_changeset_revision | status | error_message > ----+----------------------+-----------+---------+------------------------------+-------------+--------------- > 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1 > | Uninstalled | > 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303 > | New | > 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3 > | New | > (3 rows) > ************************ > How should I proceed ? > > > This is the second time I experience this. On a last note: I have noted also > that I managed to get a repository with different branches in this tool shed > repository, by mixing 'hg push' and uploading a tarball. There seems no easy > way to fixing this. > > > Kind regards, > Joachim
Hmm - do these "New" entries show up in white on the "Manage installed tool shed repositories" admin page? It sounds like a case of what was nicknamed "white ghosts", some causes of which have been fixed - but I don't think there was any automated removal of old "white ghosts" (I still have two on my test system). Peter ___________________________________________________________ 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/
