class GeneValidator::GVArgValidation::Blast
Validates BLAST Installation (And BLAST databases)
Constants
- EXIT_BLAST_NOT_COMPATIBLE
- EXIT_BLAST_NOT_INSTALLED
Use the following exit codes, or 1.
- EXIT_NO_BLAST_DATABASE
- MINIMUM_BLAST_VERSION
Use a fixed minimum version of BLAST+
Public Class Methods
assert_blast_installation()
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# File lib/genevalidator/arg_validation.rb, line 145 def assert_blast_installation # Validate BLAST installation assert_blast_installed assert_blast_compatible end
assert_local_blast_database_exists(db)
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# File lib/genevalidator/arg_validation.rb, line 151 def assert_local_blast_database_exists(db) return if system("blastdbcmd -db #{db} -info > /dev/null 2>&1") warn '*** No BLAST database found at the provided path.' warn ' Please ensure that the provided path is correct' \ ' and then try again.' exit EXIT_NO_BLAST_DATABASE end
validate(opt)
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# File lib/genevalidator/arg_validation.rb, line 140 def validate(opt) assert_blast_installation assert_local_blast_database_exists(opt[:db]) if opt[:db] !~ /remote/ end
Private Class Methods
assert_blast_compatible()
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# File lib/genevalidator/arg_validation.rb, line 167 def assert_blast_compatible version = `blastdbcmd -version`.split[1] return if version >= MINIMUM_BLAST_VERSION warn "*** Your BLAST+ version #{version} is outdated." warn ' GeneValidator needs NCBI BLAST+ version' \ " #{MINIMUM_BLAST_VERSION} or higher." exit EXIT_BLAST_NOT_COMPATIBLE end
assert_blast_installed()
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# File lib/genevalidator/arg_validation.rb, line 161 def assert_blast_installed return if GVArgValidation.command?('blastdbcmd') warn '*** Could not find BLAST+ binaries.' exit EXIT_BLAST_NOT_INSTALLED end