On Tue, Sep 25, 2012 at 8:39 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tuesday, September 25, 2012, Liisa Koski wrote:
>>
>> Hello,
>> I followed the instructions below to manually install the blast_datatypes:
>>
>> Manual Installation
>> ===================
>>
>> Normally you would install this via the Galaxy ToolShed, which would move
>> the provided blast.py file into a suitable location and process the
>> datatypes_conf.xml entry to be combined with your local configuration.
>>
>> However, if you really want to this should work for a manual install. Add
>> the following line to the datatypes_conf.xml file in the Galaxy main
>> folder:
>>
>>    <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml"
>> mimetype="application/xml" display_in_upload="true"/>
>>
>> Also create the file lib/galaxy/datatypes/blast.py by moving, copying or
>> linking the blast.py file provided in this tar-ball.  Finally add 'import 
>> blast'
>> near
>> the start of file lib/galaxy/datatypes/registry.py (after the other import
>> lines).
>>
>> =========================
>>
>> I restarted my local Galaxy instance but still get this error.
>>
>> 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 be much appreciated.
>> Thanks,
>> Liisa
>
>
> The error message sounds like your XML file is using the old location of the
> BlastXml class (it used to be in an xml.py file, now it is in blast.py
> instead). Can you grep the XML file for Blast? (Use -I for case insensitive)
>
> Sadly right now our Galaxy server is offline (suspected disk failure), so I
> may not be able to double check what is on our machine. I'll try to have a
> look at work tomorrow though.

My guess is you have this, with an out of date sniffer line from when
BLAST+ was part of the main distribution:

    <datatype extension="blastxml"
type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml"
display_in_upload="true"/>
    <sniffer type="galaxy.datatypes.xml:BlastXml"/>

And you should have:

$ grep -i blast datatypes_conf.xml
    <datatype extension="blastxml"
type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml"
display_in_upload="true"/>
    <sniffer type="galaxy.datatypes.blast:BlastXml"/>

Or, if you leave out the sniffer:

$ grep -i blast datatypes_conf.xml
    <datatype extension="blastxml"
type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml"
display_in_upload="true"/>

The sniffer is important to allow the user to upload BLAST XML files
and have them automatically recognised as such. I see that I had not
mentioned that in the tool's README file, an oversight I will fix in the
next upload to the tool shed:
https://bitbucket.org/peterjc/galaxy-central/changeset/5cefd5d5536ea9bc11021c4c1e0b8937175e4ba1

> (Out of interest, was there a reason you didn't use the automatic install
> from the ToolShed?)

I should probably have also checked - are you running a recent
version of Galaxy where the NCBI BLAST+ wrappers have been
removed from the core distribution?

Regards,

Peter
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