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';
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
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