diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/biobambam2/package.py | 21 |
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 |