biobambam2: Add test method and test scripts. (#21504)

Co-Authored-By: Tamara Dahlgren <dahlgren1@llnl.gov>

1 files changed, 20 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/biobambam2/package.py b/var/spack/repos/builtin/packages/biobambam2/package.py
index 79b7269384..bafad81657 100644
--- a/var/spack/repos/builtin/packages/biobambam2/package.py
+++ b/var/spack/repos/builtin/packages/biobambam2/package.py
@@ -21,6 +21,26 @@ class Biobambam2(AutotoolsPackage):
     depends_on('m4',       type='build')
     depends_on('libmaus2')
 
+    test_src_dir = 'test'
+
     def configure_args(self):
         args = ['--with-libmaus2={0}'.format(self.spec['libmaus2'].prefix)]
         return args
+
+    def _fix_shortsort(self):
+        """Fix the testshortsort.sh file copied during installation."""
+        test_dir = join_path(self.install_test_root, self.test_src_dir)
+        filter_file('../src/', '', join_path(test_dir, 'testshortsort.sh'))
+
+    @run_after('install')
+    def cache_test_sources(self):
+        """Copy the test source files after the package is installed to an
+        install test subdirectory for use during `spack test run`."""
+        self.cache_extra_test_sources(self.test_src_dir)
+        self._fix_shortsort()
+
+    def test(self):
+        test_dir = join_path(self.install_test_root, self.test_src_dir)
+        self.run_test('sh', ['testshortsort.sh'],
+                      expected='Alignments sorted by coordinate.',
+                      work_dir=test_dir)