old_contents: # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  import os.path
  
  
  class Varscan(Package):
      """Variant calling and somatic mutation/CNV detection for next-generation
         sequencing data"""
  
      homepage = "http://dkoboldt.github.io/varscan/"
      url      = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
  
      version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False)
  
      depends_on('java', type=('build', 'run'))
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.jar)
          jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted)
          install(jar_file, prefix.jar)
  
          script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
          script = prefix.bin.varscan
          install(script_sh, script)
          set_executable(script)
  
          java = join_path(self.spec['java'].prefix, 'bin', 'java')
          kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
          filter_file('^java', java, script, **kwargs)
          filter_file('varscan.jar', join_path(prefix.jar, jar_file),
                      script, **kwargs)
  
      def setup_environment(self, spack_env, run_env):
          run_env.set('VARSCAN_HOME', self.prefix)
          run_env.set('CLASSPATH', self.prefix.jar)
  
new_contents: # Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  import os.path
  
  
  class Varscan(Package):
      """Variant calling and somatic mutation/CNV detection for next-generation
         sequencing data"""
  
      homepage = "http://dkoboldt.github.io/varscan/"
      url      = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
  
      version('2.4.2', '4b810741505a8145a7f8f9f6791bbacf', expand=False)
  
      depends_on('java', type=('build', 'run'))
  
      def install(self, spec, prefix):
          mkdirp(prefix.bin)
          mkdirp(prefix.jar)
          jar_file = 'VarScan.v{v}.jar'.format(v=self.version.dotted)
          install(jar_file, prefix.jar)
  
          script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
          script = prefix.bin.varscan
          install(script_sh, script)
          set_executable(script)
  
          java = join_path(self.spec['java'].prefix, 'bin', 'java')
          kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
          filter_file('^java', java, script, **kwargs)
          filter_file('varscan.jar', join_path(prefix.jar, jar_file),
                      script, **kwargs)
  
      def setup_environment(self, spack_env, run_env):
          run_env.set('VARSCAN_HOME', self.prefix.jar)
          run_env.set('CLASSPATH', self.prefix.jar)
  
subject: set VARSCAN_HOME variable to jar file location (#10744)