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.

1 files changed, 11 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py
index bac7eb8377..e1c49d2cb0 100644
--- a/var/spack/repos/builtin/packages/repeatmasker/package.py
+++ b/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 @@ class Repeatmasker(Package):
                                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 @@ class Repeatmasker(Package):
             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)