The cloud admin interface's automatic update mechanism doesn't currently support toolshed updates due to the interaction required. At this point, if you're updating a cloud instance you'll need to do it manually. SSH in, switch to the galaxy user, navigate to /mnt/galaxyTools/galaxy-central, and perform an hg pull and update as usual, following all of the instructions printed to the command line (including adding tool_config_file, etc.)
We'll definitely streamline this going forward, but for now if you want to update you have to do it manually.
Dannon
On Aug 29, 2012, at 7:01 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
Hi Mohammad,
Don't forget to CC the mailing list ;)
It sounds like something has gone wrong with the update...
Peter
On Wednesday, August 29, 2012, Mohammad Heydarian wrote: Hi Peter, Thanks for your response.
I am not using any of the Blast tools, I have only tried using the "filter and sort" and "text manipulation" tools and gotten this error.
Could this be fixed by re-updating my instance of Galaxy Cloudman? Or some similar fix? I am not able to install tools to my instance of Galaxy Cloudman, the error I get is: The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a <toolbox> tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is <toolbox tool_path="../shed_tools">).
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205
On Wed, Aug 29, 2012 at 3:24 PM, Peter Cock p.j.a.cock@googlemail.com wrote: Hi
The BLAST+ tools and the definition of the blastxml format were moved to the tool shed. You should have seen a migration message during the update...
If you are not using these tools, perhaps you have a legacy reference to the blastxml file which should be removed?
If you are using BLAST+ they and the blastxml format need to be installed from the ToolShed,
Peter
On Wednesday, August 29, 2012, Mohammad Heydarian wrote: Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error:
WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml'
Any help would greatly be appreciated.
Cheers, Mo Heydarian
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