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-rw-r--r--var/spack/repos/builtin/packages/biobambam2/package.py21
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