CommandLineBlast.scala.java

object CommandLineBlast {
  lazy val blastHome = getenv("BLAST_HOME")
  lazy val tmpDir = getProperty("java.io.tmpdir")

  def blast(config: BlastConfiguration): AnalysisResult = {
    if (blastHome == null) {
      error("BLAST_HOME is not defined. It must point to the BLAST installation directory, e.g. BLAST_HOME=/opt/blast")
    } else {
      val executable = blastHome + "/bin/" + config.searchUtility.name
      val c = command(executable)("-p", config.program.name)("-e 1.0")("-d ecoli.nt")("-i test.txt")("-o test.out")
      val p = c.executeInDir(blastHome)
      println(p.output)
      BlastAnalysisResult("Huzzah!")
    }
  }
}