Hi Greg, Thanks for this!
On 17 October 2012 01:17, Greg Von Kuster <g...@bx.psu.edu> wrote: >> I managed to break a toolshed-installed tool by fiddling with the >> files under shed_tools. > > As you've discovered, this is not a good thing to try. Always use the Galaxy > interface features to perform tasks like this. > Actually, the reason I did this was because I didn't know how to solve a different problem, so maybe I should ask you about that one as well. We had some occasions where we'd try to install a tool from the toolshed, and it would hang - it appeared that the hg pull was timing out. In these cases the config files wouldn't get set up, but a partial repository was pulled / directories were created, and the repository files would then get in the way of trying to install the tool (it seemed to think it was already there). The only way to fix it seemed to be to manually delete the partially-pulled repository under shed_tools. This worked fine for fixing failed installs. But, this time, I thought (wrongly) that this had happened again and I deleted a repository - then realised that it was actually installed and registered in the database, etc. So, if the hg pull times out, is there a right way to clean up the resulting files? I got in the habit of doing it manually, which of course is dangerous, because I didn't know any way to do it via the admin interface. > > Depending on the changes you've made, you should be able to do the following: > > 1. Manually remove the installed repository subdirectory hierarchy from disk. > 2. If the repository included any tools, manually remove entries for each of > them from the shed_tool-conf.xml file ( or the equivalent file you have > configured for handling installed repositories ) > 3. Manually update the database using the following command (assuming your > installed repository is named 'bcftools_view' and it is the only repository > you have installed with that name) - letter capitalization is required: > > The following assumes you're using postgres: > > update tool_shed_repository set deleted=True, uninstalled=True, > status='Uninstalled', error_message=Null where name = 'bcftools_view'; > Thanks very much! Yes it's postgres. I'll let you know if I succeed. Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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/
