On Tuesday, September 25, 2012, Liisa Koski wrote:

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Hello, I followed the instructions below to manually install the

blast_datatypes:

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Manual Installation ===================

Normally you would install this via the Galaxy ToolShed, which would

move

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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).

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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

Thanks Peter, It was in fact the snffier type. I changed it to <sniffer type="galaxy.datatypes.blast:BlastXml"/> I am using the July07 distribution. The reason I installed the datatypes manually is because when I did it via the directions with the toolshed all my workflows that used blast tools were broken. They could no longer find the blast tools. So I immediately removed the toolshed installation and tried to set up as before. With the blast wrappers back in the tools/ncbi_blast_plus directory. Now my workflows are functional again. Thanks for your help, Liisa From: Peter Cock <p.j.a.cock@googlemail.com> To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu> Cc: Liisa Koski <liisa.koski@basf.com> Date: 26/09/2012 04:33 AM Subject: Re: [galaxy-dev] problem installing blast_datatypes manually On Tue, Sep 25, 2012 at 8:39 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote: 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/5cefd5d5536ea9bc11021...

(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

Hi Liisa and Peter, There was an issue if your workflows were created using the ncbi blast tools from the distribution (e.g. versions 0.0.11) and you only had installed the latest tools from the toolshed (e.g. versions 0.0.13). This has been corrected in changesets 7754:371f6770d25c through 7756:c76e2882d2d2 and will be available in the next distribution. Please let us know if you are still experiencing issues after the update us released. The preferred method for handling tools that have been migrated is to use the provided migration scripts (in this case ' sh ./scripts/migrate_tools/0004_tools.sh' or 'sh ./scripts/migrate_tools/0004_tools.sh install_dependencies') and then starting the Galaxy server; after running the migrations to get the original tool versions installed, you can then install the the newest versions of the tools via the admin interface. However, using the migration scripts is optional, and you can always install the original tools via the admin interface, or manually, if that is desired. Thanks for using Galaxy, Dan On Sep 26, 2012, at 9:29 AM, Peter Cock wrote:

On Wed, Sep 26, 2012 at 2:20 PM, Liisa Koski <liisa.koski@basf.com> wrote:

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Thanks Peter, It was in fact the snffier type. I changed it to <sniffer type="galaxy.datatypes.blast:BlastXml"/>

And its all working now (as far as you can tell)?

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I am using the July07 distribution. The reason I installed the datatypes manually is because when I did it via the directions with the toolshed all my workflows that used blast tools were broken. They could no longer find the blast tools. So I immediately removed the toolshed installation and tried to set up as before. With the blast wrappers back in the tools/ncbi_blast_plus directory. Now my workflows are functional again.

That is strange - and one for the Galaxy team to puzzle over. I've not tried this myself (since I'm actively developing the BLAST+ wrappers, and often trying things before pushing them to the ToolShed for wider user, it is easier for me to install them locally via the manual route).

Thanks for your feedback,

Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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