Hi Sheldon,

I recommend not manually changing any database entries.  You should be able to 
install the repository and all of its dependencies using the Repair Repository 
feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

Greg Von Kuster

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca> 
wrote:

> Hi,
>  
> Just wondering if I can still use the following to fix up my messed up 
> tophat2 install (the install had hung up on me, for 2 hours, and I tried to 
> remove/repair it via the interface).  I haven’t had problems installing any 
> other tools or packages.  I am using postgres but this advice was given 2 
> years ago to another user and fields may have changed.  Thanks for any help!
> -Sheldon  
>  
> 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';
>  
>  
>  
> From: Briand, Sheldon 
> Sent: Wednesday, March 12, 2014 11:44 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: tophat2 install
>  
> Hi,
>  
> I ran into a problem installing tophat2 here:
> tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType 
> found
>  
> I have only used the interface to do the installation (no manual deletes).  
> The rest of the dependencies for tophat2 installed just fine.
>  
> Repairing the repository doesn’t make any difference.
>  
> Thanks!
> -Sheldon
>  
> Sheldon Briand
> NRC Research Computing Support Analyst
> Research Computing Support / Soutien Informartique a la Recherche
> Operations, Science Portfolio / Operations, Portefeuil des sciences
> SSC-NRC / SPC-CNRC
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> Halifax, NS  B3H 3Z1
> 902 426-1677
> sheldon.bri...@ssc-spc.gc.ca
>  
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