debian/control

@@ -11,6 +11,7 @@ Build-Depends: debhelper (>= 11~),
                bowtie2,
                freebayes,
                ncbi-blast+,
+               pilon,
                racon,
                samtools,
                spades,
@@ -28,6 +29,7 @@ Depends: ${python3:Depends},
          bowtie2,
          freebayes,
          ncbi-blast+,
+         pilon,
          racon,
          samtools,
          spades

debian/patches/bowtie.patch

+Description: No idea how the test suite can be convinced to find the tools
+  Asked upstream for help in
+      https://github.com/rrwick/Unicycler/issues/114
+  This patch does not really help
+
+--- a/unicycler/unicycler.py
++++ b/unicycler/unicycler.py
+@@ -411,10 +411,10 @@ def get_arguments():
+                               help='Do not use Pilon to polish the final assembly (default: Pilon '
+                                    'is used)'
+                                    if show_all_args else argparse.SUPPRESS)
+-    polish_group.add_argument('--bowtie2_path', type=str, default='bowtie2',
++    polish_group.add_argument('--bowtie2_path', type=str, default='/usr/bin/bowtie2',
+                               help='Path to the bowtie2 executable'
+                                    if show_all_args else argparse.SUPPRESS)
+-    polish_group.add_argument('--bowtie2_build_path', type=str, default='bowtie2-build',
++    polish_group.add_argument('--bowtie2_build_path', type=str, default='/usr/bin/bowtie2-build',
+                               help='Path to the bowtie2_build executable'
+                                    if show_all_args else argparse.SUPPRESS)
+     polish_group.add_argument('--samtools_path', type=str, default='samtools',
+--- a/test/test_dependencies.py
++++ b/test/test_dependencies.py
+@@ -59,13 +59,13 @@ class TestDependencies(unittest.TestCase
+         self.assertEqual(ret_code, 1)
+ 
+     def test_bowtie2_build_not_found(self):
+-        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', 'not_a_real_path'])
++        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', '/usr/bin'])
+         self.assertTrue(bool(re.search(r'bowtie2-build\s+not found', stdout)))
+         self.assertTrue('could not find bowtie2-build' in stderr)
+         self.assertEqual(ret_code, 1)
+ 
+     def test_bowtie2_not_found(self):
+-        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', 'not_a_real_path'])
++        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', '/usr/bin'])
+         self.assertTrue(bool(re.search(r'bowtie2\s+not found', stdout)))
+         self.assertTrue('could not find bowtie2' in stderr)
+         self.assertEqual(ret_code, 1)

debian/patches/series

 spades.patch
+# bowtie.patch 

debian/rules

@@ -13,6 +13,8 @@ export DH_BUILD_MAINT_OPTIONS=nocheck
 override_dh_auto_clean:
 	echo "Avoid:  command 'UnicyclerClean' has no such option 'all'"
 	find . -name "*.o" -delete
+	find . -name "*.so" -delete
+	find . -name __pycache__ -type d | xargs rm -rf
 
 override_dh_auto_build:
 	dh_auto_build
@@ -22,5 +24,6 @@ override_dh_auto_build:
 override_dh_auto_test:
 	BUILDPATH=$(shell pybuild --print build_dir --interpreter python3) ; \
 	ln -s $(CURDIR)/sample_data $${BUILDPATH} ; \
+	ln -s $(CURDIR)/unicycler-runner.py $${BUILDPATH} ; \
 	cp -a unicycler/*.so $${BUILDPATH}/$(PYBUILD_NAME) ; \
 	PYTHONPATH=$${BUILDPATH}/$(PYBUILD_NAME) dh_auto_test