sam to bam in galaxy

Question: sam to bam in galaxy

2.8 years ago by

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 • 884 views

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modified 2.8 years ago • written 2.8 years ago by snehalbpatil87 • 30

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 REPLY • link written 2.8 years ago by Hotz, Hans-Rudolf • 1.8k

2.8 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k 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 COMMENT • link written 2.8 years ago by Hotz, Hans-Rudolf • 1.8k

2.8 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 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,

ADD COMMENT • link written 2.8 years ago by snehalbpatil87 • 30

2.8 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 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 COMMENT • link written 2.8 years ago by snehalbpatil87 • 30

"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 REPLY • link written 2.8 years ago by Hotz, Hans-Rudolf • 1.8k

2.8 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 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

ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by snehalbpatil87 • 30

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

Hans-Rudolf

ADD REPLY • link written 2.8 years ago by Hotz, Hans-Rudolf • 1.8k

2.8 years ago by

snehalbpatil87 • 30

snehalbpatil87 • 30 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 COMMENT • link written 2.8 years ago by snehalbpatil87 • 30

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 REPLY • link written 2.8 years ago by Hotz, Hans-Rudolf • 1.8k

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