Fwd: Adding custom genome

11 Mar 2010

      Hi

I just noticed (after a history refresh) that when I try to use a GFF3 
file to extract genomic DNA a job is created that converts the GFF to 
BED. Using the GFF file directly gives the error I detailed earlier (see 
below) but using the BED file works fine and I get the genomic sequence 
I want.

If I first convert the GFF to a BED file everything is also fine (as 
expected from the above).

So, it looks as though the problem is actually associated with the 
process of GFF-->BED-->extract genomic and not the actual extraction of 
sequences.

Has anyone else seen this behaviour?

Thanks

Nathaniel

-------- Original Message --------
Subject: Adding custom genome
Date: Thu, 11 Mar 2010 14:24:13 +0100
From: Nathaniel Street <nathaniel.street@plantphys.umu.se>
To: galaxy-dev@lists.bx.psu.edu

Hi

I'm trying to add a custom genome to a local galaxy install. So far I
have done this:

1)Create a fasta file per scaffold (it's an unfinished genome)
2)Create a nib file per one of those scaffold fasta files
3)Add an entry to build.txt
nis    Test genome (nis)
4)Add a line to alignseq.loc
seq    nis    /data/nib/nis
5)Add a line to faseq.loc
nis    /data/sequences/nis

Is there more that I need to do to be able to extract sequences using
the Extract Genomic DNA tool?

I tried to use the tool by uploading a GFF3 file, extracting a small
part of that for testing and then using that small part to extract
genomic DNA. When I try this I get an error message returned

AttributeError: 'tuple' object has no attribute 'iteritems'

And the text version of the Traceback gives this

URL: http://XXX:XXX:XX:XX:8080/tool_runner/index
File
'/home/nat/work/software/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', 

line 364 in respond
   app_iter = self.application(environ, detect_start_response)
File
'/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', 

line 98 in __call__
   environ, self.app)
File
'/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 

line 539 in intercept_output
   app_iter = application(environ, replacement_start_response)
File
'/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 

line 80 in __call__
   return self.application(environ, start_response)
File
'/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 

line 632 in __call__
   return self.application(environ, start_response)
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/web/framework/base.py',
line 125 in __call__
   body = method( trans, **kwargs )
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', 

line 53 in index
   template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py',
line 807 in handle_input
   _, out_data = self.execute( trans, incoming=params )
File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py',
line 1079 in execute
   return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid )
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py',
line 140 in execute
   inp_data = self.collect_input_datasets( tool, incoming, trans )
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py',
line 101 in collect_input_datasets
   tool.visit_inputs( param_values, visitor )
File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py',
line 754 in visit_inputs
   callback( "", input, value[input.name] )
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py',
line 85 in visitor
   input_datasets[ prefix + input.name ] = process_dataset( value )
File
'/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py',
line 47 in process_dataset
   new_data = data.datatype.convert_dataset( trans, data, target_ext,
return_output = True, visible = False ).values()[0]
File '/home/nat/work/software/galaxy-dist/lib/galaxy/datatypes/data.py',
line 264 in convert_dataset
   for name, value in converted_dataset.iteritems():
AttributeError: 'tuple' object has no attribute 'iteritems'

Can anyone tell me what I'm doing wrong? Do I need more than only the
nib files?

Many thanks

Nathaniel
-- 
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
University of Umeå
SE-901 87 Umeå
SWEDEN

email: nathaniel.street@plantphys.umu.se
tel: +46-90-786 5473
fax:  +46-90-786 6676

www.popgenie.org

-- 
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
University of Umeå
SE-901 87 Umeå
SWEDEN

email: nathaniel.street@plantphys.umu.se
tel: +46-90-786 5473
fax:  +46-90-786 6676

www.popgenie.org

Nathaniel Street

Daniel Blankenberg

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