repeatmasker: perl and HMMER dependency fixes (#11660)

repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.

var/spack/repos/builtin/packages/repeatmasker/package.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import glob
 
 
 class Repeatmasker(Package):
@@ -71,6 +72,11 @@ def install(self, spec, prefix):
                                self.spec['ncbi-rmblastn'].prefix.bin,
                                'Y'])
 
+        # set non-default HMMER search
+        config_answers.extend(['3',
+                               self.spec['hmmer'].prefix,
+                               'N'])
+
         # end configuration
         config_answers.append('5')
 
@@ -83,4 +89,9 @@ def install(self, spec, prefix):
             perl = which('perl')
             perl('configure', input=f)
 
+        # fix perl paths
+        # every sbang points to perl, so a regex will suffice
+        for f in glob.glob('*.pm'):
+            filter_file('#!.*', '#!%s' % spec['perl'].command, f)
+
         install_tree('.', prefix.bin)