tests/biobambam2: convert to new stand-alone test process (#35696)

1 files changed, 6 insertions, 15 deletions

diff --git a/var/spack/repos/builtin/packages/biobambam2/package.py b/var/spack/repos/builtin/packages/biobambam2/package.py
index 83f90cf615..718030f85e 100644
--- a/var/spack/repos/builtin/packages/biobambam2/package.py
+++ b/var/spack/repos/builtin/packages/biobambam2/package.py
@@ -30,25 +30,16 @@ class Biobambam2(AutotoolsPackage):
         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):
-        """Perform stand-alone/smoke test on installed package."""
+    def test_short_sort(self):
+        """run testshortsort.sh to check alignments sorted by coordinate"""
         test_dir = join_path(self.test_suite.current_test_cache_dir, self.test_src_dir)
-        self.run_test(
-            "sh",
-            ["testshortsort.sh"],
-            expected="Alignments sorted by coordinate.",
-            purpose="test: checking alignments",
-            work_dir=test_dir,
-        )
+        with working_dir(test_dir):
+            sh = which("sh")
+            out = sh("testshortsort.sh", output=str.split, error=str.split)
+            assert "Alignments sorted by coordinate." in out