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.c...@googlemail.com<javascript:_e({}, 'cvml',
> 'p.j.a.c...@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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