From 4c396d2cee31edb1a2a3620a42ba2e9f5e9090bc Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Fri, 11 Feb 2022 03:30:36 -0500
Subject: [PATCH] minc-toolkit: fix perl dependencies (#28868)

---
 .../builtin/packages/minc-toolkit/package.py  |  8 +++++++-
 .../packages/perl-mni-perllib/no-stdin.patch  | 13 ++++++++++++
 .../packages/perl-mni-perllib/package.py      | 20 +++++++++++++++++++
 3 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin/packages/perl-mni-perllib/no-stdin.patch
 create mode 100644 var/spack/repos/builtin/packages/perl-mni-perllib/package.py

diff --git a/var/spack/repos/builtin/packages/minc-toolkit/package.py b/var/spack/repos/builtin/packages/minc-toolkit/package.py
index be63cf6a7f..5dfc62f193 100644
--- a/var/spack/repos/builtin/packages/minc-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/minc-toolkit/package.py
@@ -21,6 +21,12 @@ class MincToolkit(CMakePackage):
             description="Build visual tools (Display, register, etc.)")
 
     depends_on('perl')
+    # included Perl packages are not added to the Perl path by default.
+    # rather than inheriting from both CMakePackage and PerlPackage,
+    # it seems clean just to add them as dependencies:
+    depends_on('perl-text-format', type=('build', 'run'))
+    depends_on('perl-getopt-tabular', type=('build', 'run'))
+    depends_on('perl-mni-perllib', type=('build', 'run'))
     depends_on('flex', type='build')
     depends_on('bison', type='build')
     depends_on('zlib', type='link')
@@ -31,7 +37,7 @@ def cmake_args(self):
                 self.define_from_variant('MT_BUILD_VISUAL_TOOLS', 'visualisation'),
                 # newer ANTs packaged separately
                 "-DMT_BUILD_ANTS=OFF",
-                # build error; should package newer c3d separately
+                # newer c3d packaged separately
                 "-DMT_BUILD_C3D=OFF",
                 # should be packaged separately with newer ITK
                 "-DMT_BUILD_ELASTIX=OFF"
diff --git a/var/spack/repos/builtin/packages/perl-mni-perllib/no-stdin.patch b/var/spack/repos/builtin/packages/perl-mni-perllib/no-stdin.patch
new file mode 100644
index 0000000000..1e9e791257
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-mni-perllib/no-stdin.patch
@@ -0,0 +1,13 @@
+diff --git a/Makefile.PL b/Makefile.PL
+index 9f2039a..12d699c 100644
+--- a/Makefile.PL
++++ b/Makefile.PL
+@@ -213,7 +213,7 @@ TEXT
+ }  # &MY::postamble
+ 
+ 
+-query_subs;
++#query_subs;
+ 
+ my $f;
+ WriteMakefile 
diff --git a/var/spack/repos/builtin/packages/perl-mni-perllib/package.py b/var/spack/repos/builtin/packages/perl-mni-perllib/package.py
new file mode 100644
index 0000000000..5c372c52b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-mni-perllib/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2022 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 *
+
+
+class PerlMniPerllib(PerlPackage):
+    """MNI Perl Library for scripting long-running scientific computations"""
+
+    homepage = "https://github.com/BIC-MNI/mni-perllib"
+    git      = "https://github.com/BIC-MNI/mni-perllib.git"
+
+    version('develop', commit="170827f5644820b87bcb2b194494c5ebf0928149")
+
+    patch('no-stdin.patch')
+
+    depends_on('perl-getopt-tabular', type=('build', 'run'))
+    depends_on('perl-text-format', type=('build', 'run'))