Module: Quorum

Defined in:
lib/quorum.rb,
lib/quorum/engine.rb,
lib/quorum/helpers.rb,
lib/quorum/version.rb,
lib/quorum/sequence.rb,
app/models/quorum/job.rb,
app/models/quorum/blastn_job.rb,
app/models/quorum/blastp_job.rb,
app/models/quorum/blastx_job.rb,
app/models/quorum/tblastn_job.rb,
lib/generators/templates/blast.rb,
lib/generators/templates/logger.rb,
lib/tasks/blastdb/build_blast_db.rb,
lib/generators/templates/blast_db.rb,
app/models/quorum/blastn_job_report.rb,
app/models/quorum/blastp_job_report.rb,
app/models/quorum/blastx_job_report.rb,
app/models/quorum/tblastn_job_report.rb,
app/helpers/quorum/application_helper.rb,
lib/generators/quorum/views_generator.rb,
app/controllers/quorum/jobs_controller.rb,
lib/generators/quorum/images_generator.rb,
lib/generators/quorum/styles_generator.rb,
lib/generators/quorum/install_generator.rb,
app/controllers/quorum/application_controller.rb

Defined Under Namespace

Modules: ApplicationHelper, FetchTools, Generators, Helpers, SearchTools, Sequence Classes: ApplicationController, BlastnJob, BlastnJobReport, BlastpJob, BlastpJobReport, BlastxJob, BlastxJobReport, BuildBlastDB, Engine, Job, JobsController, Logger, TblastnJob, TblastnJobReport

Constant Summary collapse

BLAST_ALGORITHMS =

Supported Algorithms ##

["blastn", "blastx", "blastp", "tblastn"].freeze
VERSION = 
"0.7.0"

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.blast_bin ⇒ Object

Blast bin path.



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# File 'lib/quorum.rb', line 56

def blast_bin
  @@blast_bin || nil
end

.blast_db ⇒ Object

Blast database path.



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# File 'lib/quorum.rb', line 71

def blast_db
  @@blast_db || nil
end

.blast_log_dir ⇒ Object

Blast log dir path.



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# File 'lib/quorum.rb', line 61

def blast_log_dir
  @@blast_log_dir || nil
end

.blast_remote ⇒ Object

Execute remotely.



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# File 'lib/quorum.rb', line 36

def blast_remote
  @@blast_remote || false
end

.blast_script ⇒ Object

Blast Deprecated ##



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# File 'lib/quorum.rb', line 102

def blast_script
  nil
end

.blast_ssh_host ⇒ Object

Net::SSH host.



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# File 'lib/quorum.rb', line 41

def blast_ssh_host
  @@blast_ssh_host || nil
end

.blast_ssh_options ⇒ Object

Net::SSH options.



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# File 'lib/quorum.rb', line 51

def blast_ssh_options
  @@blast_ssh_options || {}
end

.blast_ssh_user ⇒ Object

Net::SSH user.



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# File 'lib/quorum.rb', line 46

def blast_ssh_user
  @@blast_ssh_user || nil
end

.blast_threads ⇒ Object

Number of Blast threads.



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# File 'lib/quorum.rb', line 96

def blast_threads
  @@blast_threads || 1
end

.blast_tmp_dir ⇒ Object

Blast tmp dir path.



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# File 'lib/quorum.rb', line 66

def blast_tmp_dir
  @@blast_tmp_dir || nil
end

.blastn ⇒ Object

blastn directories.



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# File 'lib/quorum.rb', line 86

def blastn
  @@blastn || []
end

.blastp ⇒ Object

blastp directories.



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# File 'lib/quorum.rb', line 81

def blastp
  @@blastp || []
end

.blastx ⇒ Object

blastx directories.



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# File 'lib/quorum.rb', line 91

def blastx
  @@blastx || []
end

.max_sequence_size ⇒ Object

Max input sequence size.



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# File 'lib/quorum.rb', line 29

def max_sequence_size
  @@max_sequence_size || 50.kilobytes
end

.tblastn ⇒ Object

tblastn directories.



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# File 'lib/quorum.rb', line 76

def tblastn
  @@tblastn || []
end

Instance Method Details

#blast_script ⇒ Object

Deprecated ##



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# File 'lib/quorum.rb', line 22

mattr_accessor :blast_script