Module: NeuroHmmerApp::RunNeuroHmmer

Extended by:
Forwardable
Defined in:
lib/neurohmmerapp/neurohmmer.rb

Overview

Module that runs NeuroHmmer

Defined Under Namespace

Classes: ArgumentError, RuntimeError

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.gv_dir ⇒ Object (readonly)

Returns the value of attribute gv_dir.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def gv_dir
  @gv_dir
end

.input_file ⇒ Object (readonly)

Returns the value of attribute input_file.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def input_file
  @input_file
end

.params ⇒ Object (readonly)

Returns the value of attribute params.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def params
  @params
end

.raw_seq ⇒ Object (readonly)

Returns the value of attribute raw_seq.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def raw_seq
  @raw_seq
end

.unique_id ⇒ Object (readonly)

Returns the value of attribute unique_id.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def unique_id
  @unique_id
end

.xml_file ⇒ Object (readonly)

Returns the value of attribute xml_file.



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 27

def xml_file
  @xml_file
end

Class Method Details

.init(_base_url, params) ⇒ Object

Setting the scene



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 30

def init(_base_url, params)
  create_unique_id
  create_run_dir
  @params = params
  validate_params
  # @url = produce_result_url_link(base_url)
end

.run ⇒ Object

Runs genevalidator & Returns parsed JSON, or link to JSON/results file



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# File 'lib/neurohmmerapp/neurohmmer.rb', line 39

def run
  write_seqs_to_file
  run_neurohmmer
end