Update genemark-et package

- add version 4.46
- add missing perl dependencies
- new version has different source layout
- filter shebang to use spack perl

var/spack/repos/builtin/packages/genemark-et/package.py

@@ -19,10 +19,15 @@ class GenemarkEt(Package):
 
     homepage = "http://topaz.gatech.edu/GeneMark"
 
+    version('4.46', sha256='856b0b6c7cbd12835e140ff04ecd9124376348efd65f76bfd8b8e08c1834eac0')
     version('4.38', sha256='cee3bd73d331be44159eac15469560d0b07ffa2c98ac764c37219e1f3b7d3146')
     version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3')
 
     depends_on('perl', type=('build', 'run'))
+    depends_on('perl-yaml', type=('build', 'run'))
+    depends_on('perl-hash-merge', type=('build', 'run'))
+    depends_on('perl-logger-simple', type=('build', 'run'))
+    depends_on('perl-parallel-forkmanager', type=('build', 'run'))
 
     def url_for_version(self, version):
         return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd())
@@ -30,7 +35,11 @@ def url_for_version(self, version):
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         mkdirp(prefix.bin.heu_dir)
-        with working_dir('gmes_petap'):
+        if self.version <= Version('4.38'):
+            source_dir = 'gmes_petap'
+        else:
+            source_dir = self.stage.source_path
+        with working_dir(source_dir):
             install_tree('lib', prefix.lib)
             files = glob.iglob('*')
             for file in files:
@@ -38,5 +47,14 @@ def install(self, spec, prefix):
                     install(file, prefix.bin)
             install_tree('heu_dir', prefix.bin.heu_dir)
 
+    @run_after('install')
+    def filter_sbang(self):
+        with working_dir(self.prefix.bin):
+            pattern = '^#!.*/usr/bin/perl'
+            repl = '#!{0}'.format(self.spec['perl'].command.path)
+            files = glob.iglob("*.pl")
+            for file in files:
+                filter_file(pattern, repl, *files, backup=False)
+
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PERL5LIB', prefix.lib)