Question: sam to bam in galaxy
0
gravatar for snehalbpatil87
22 months ago by
snehalbpatil8730 wrote:

Has anyone tried to implement sam to bam in local galaxy instance? iam trying having difficulty in reference genome? Can anyone guide me please?

sam to bam • 578 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by snehalbpatil8730

Hi

what do you mean by 'implement sam to bam'? Are you refering to the tool 'sam_to_bam' which you can get from the toolshed, or have you written your own wrapper?

Also, in order to better help you, provide any error messages you get.

Hans-Rudolf

 

 


 

ADD REPLYlink written 22 months ago by Hotz, Hans-Rudolf1.7k
1
gravatar for Hotz, Hans-Rudolf
22 months ago by
Switzerland
Hotz, Hans-Rudolf1.7k wrote:

Hi SP

 

First, make sure the dbkey of your sam file which you have selected, has at least one entry in the "fasta_indexes.loc" file.

Second, you might need to add

    <table name="fasta_indexes" comment_char="#">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/fasta_indexes.loc" />
    </table>

to the "tool_data_table_conf.xml" file.

 

Regards, Hans-Rudolf

ADD COMMENTlink written 22 months ago by Hotz, Hans-Rudolf1.7k
0
gravatar for snehalbpatil87
22 months ago by
snehalbpatil8730 wrote:

I am trying to implement sam to bam in my local instance. I installed it from Tool Shed. Do I have to do any additional setting for Reference genome. When I try to submit  without that reference genome, it gives me please verify the parameter. I checked fasta_index.loc it has correct setting for .fa file.

 

Thanks,

SP

ADD COMMENTlink written 22 months ago by snehalbpatil8730
0
gravatar for snehalbpatil87
22 months ago by
snehalbpatil8730 wrote:

Hello Hans-Rudolf:

Can you please explain on dbkey of your sam file. ..I thought fasta_indexe contains link to .fa file

I wrote following line to .loc file.

hg19    hg19    Human (hg19)    /home/snehal/Galaxy/hg19/bowtie_path/base/genome.fa

 

ADD COMMENTlink written 22 months ago by snehalbpatil8730

"dbkey of your sam file": 

In your history, click on the sam file which you want to selected. You will see: 'format sam database XX'. What is XX in your case? It needs to be one of the dbkeys you have listed in your fasta_indexes.loc files (e.g. hg19).

Regards, Hans-Rudolf

ADD REPLYlink written 22 months ago by Hotz, Hans-Rudolf1.7k
0
gravatar for snehalbpatil87
22 months ago by
snehalbpatil8730 wrote:

Hello Hans-Rudolf:

Thank you for yr  response. But My galaxy tool is giving me below error today. I am not able to figure out what went wrong.

 

URL: http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsam_to_bam%2Fsam_to_bam%2F2.1
File '/home/snehal/Galaxy/galaxy/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/snehal/Galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/home/snehal/Galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/home/snehal/Galaxy/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/web/framework/base.py', line 191 in handle_request
  body = method( trans, **kwargs )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 96 in index
  template, vars = tool.handle_input( trans, params.__dict__ )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1295 in handle_input
  state, state_new = self.__fetch_state( trans, expanded_incoming, history, all_pages=all_pages )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1410 in __fetch_state
  state = self.new_state( trans, history=history, all_pages=all_pages )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1191 in new_state
  self.fill_in_new_state( trans, inputs, state.inputs, history=history )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/__init__.py', line 1201 in fill_in_new_state
  state[ input.name ] = input.get_initial_value( trans, context, history=history )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py', line 627 in get_initial_value
  rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=history )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/basic.py', line 983 in get_initial_value
  options = list( self.get_options( trans, context ) )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/basic.py', line 840 in get_options
  return self.options.get_options( trans, other_values )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py', line 637 in get_options
  options = self.get_fields( trans, other_values )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py', line 603 in get_fields
  options = filter.filter_options( options, trans, other_values )
File '/home/snehal/Galaxy/galaxy/lib/galaxy/tools/parameters/dynamic_options.py', line 151 in filter_options
  return [ ( disp_name, basic.UnvalidatedValue( optval ), selected ) for disp_name, optval, selected in options ]
ValueError: too many values to unpack

 

DO you know anything about this error.

 

Thanks

SP

ADD COMMENTlink modified 22 months ago • written 22 months ago by snehalbpatil8730

one step after the other: do you now have value(s) in the drop down?

Hans-Rudolf

 

ADD REPLYlink written 22 months ago by Hotz, Hans-Rudolf1.7k
0
gravatar for snehalbpatil87
22 months ago by
snehalbpatil8730 wrote:

Hello Has-Rudolf:

Yes. Choose the source for the reference genome..

1.I was creating my own wrapper and I had also the copy of the sam_to_bam tool shed version. Once I deleted my wrapper and reinstalled the tool from toolshed version of sam_to_bam , error disappeared . Were two files of the same program creating conflict?I had different names for them . Issue is solved but I am not sure how?

 

Thanks

Snehal

ADD COMMENTlink written 22 months ago by snehalbpatil8730

Hi Snehal

I am glad to hear the issue is now solved.

WRT having two different warppers: make sure they use a different "id"  in the two xml files.

Regards, Hans-Rudolf

 

 

ADD REPLYlink written 22 months ago by Hotz, Hans-Rudolf1.7k
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