Hi,

Yes the error is:
Error installing tool dependency package tophat2 version 2.0.9: coercing to 
Unicode: need string or buffer, NoneType found

-Sheldon

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
Subject: Re: [galaxy-dev] tophat2 install

You should be able to click on the missing tool dependency and see its 
installation log.  It should show you whatever error is occuring that is not 
allowing successful installation.

Greg Von Kuster

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" 
<sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:


Hi,

The repair operation doesn't seem to make any difference (I already tried that 
before emailing).  Screenshot of the result attached.

-Sheldon


From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
Subject: Re: [galaxy-dev] tophat2 install

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<mailto: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<mailto: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<mailto:sheldon.bri...@ssc-spc.gc.ca>

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