From d82f8cd405c13d2fe4cfd4221669f1c3a5b023cb Mon Sep 17 00:00:00 2001
From: Justin S <3630356+codeandkey@users.noreply.github.com>
Date: Tue, 18 Jun 2019 13:11:00 -0500
Subject: [PATCH] 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.
---
.../repos/builtin/packages/repeatmasker/package.py | 11 +++++++++++
1 file changed, 11 insertions(+)
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 @@ 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)
--
GitLab