debian/control

@@ -7,7 +7,14 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                python3-all,
                python3-setuptools,
-               spades
+               default-jdk,
+               bowtie2,
+               freebayes,
+               ncbi-blast+,
+               racon,
+               samtools,
+               spades,
+               zlib1g-dev
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/unicycler
 Vcs-Git: https://salsa.debian.org/med-team/unicycler.git
@@ -17,10 +24,13 @@ Package: unicycler
 Architecture: any
 Depends: ${python3:Depends},
          ${misc:Depends},
-         spades,
-         ncbi-blast+,
+         default-jre,
          bowtie2,
-         samtools
+         freebayes,
+         ncbi-blast+,
+         racon,
+         samtools,
+         spades
 Description: hybrid assembly pipeline for bacterial genomes
  Unicycler is an assembly pipeline for bacterial genomes. It can assemble
  Illumina-only read sets where it functions as a SPAdes-optimiser. It can

debian/patches/series

+spades.patch

debian/patches/spades.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 25 May 2018 10:59:36 +0200
+Description: SPAdes is in Debian at /usr/bin/spades
+
+--- a/test/test_dependencies.py
++++ b/test/test_dependencies.py
+@@ -42,7 +42,7 @@ class TestDependencies(unittest.TestCase
+ 
+     def test_spades_not_found(self):
+         stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path'])
+-        self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))
++        self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))
+         self.assertTrue('could not find SPAdes' in stderr)
+         self.assertEqual(ret_code, 1)
+ 
+@@ -102,14 +102,14 @@ class TestDependencies(unittest.TestCase
+     def test_no_rotate(self):
+         stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',
+                                                        '--no_rotate'])
+-        self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))
++        self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))
+         self.assertTrue(bool(re.search(r'makeblastdb\s+not used', stdout)))
+         self.assertTrue(bool(re.search(r'tblastn\s+not used', stdout)))
+ 
+     def test_no_pilon(self):
+         stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',
+                                                        '--no_pilon'])
+-        self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))
++        self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))
+         self.assertTrue(bool(re.search(r'bowtie2-build\s+not used', stdout)))
+         self.assertTrue(bool(re.search(r'bowtie2\s+not used', stdout)))
+         self.assertTrue(bool(re.search(r'samtools\s+not used', stdout)))
+@@ -119,12 +119,12 @@ class TestDependencies(unittest.TestCase
+     def test_verbosity_1(self):
+         stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',
+                                                        '--verbosity', '1'])
+-        self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))
++        self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))
+         self.assertTrue(bool(re.search(r'Program\s+Version\s+Status', stdout)))
+         self.assertFalse(bool(re.search(r'Program\s+Version\s+Status\s+Path', stdout)))
+ 
+     def test_verbosity_2(self):
+         stdout, stderr, ret_code = self.run_unicycler(['--spades_path', 'not_a_real_path',
+                                                        '--verbosity', '2'])
+-        self.assertTrue(bool(re.search(r'spades.py\s+not found', stdout)))
++        self.assertTrue(bool(re.search(r'spades\s+not found', stdout)))
+         self.assertTrue(bool(re.search(r'Program\s+Version\s+Status\s+Path', stdout)))
+--- a/test/overlap_removal_test.py
++++ b/test/overlap_removal_test.py
+@@ -94,7 +94,7 @@ def run_spades(out_dir):
+     reads_2 = os.path.join(out_dir, 'reads_2.fastq')
+     reads_unpaired = os.path.join(out_dir, 'reads_unpaired.fastq')
+ 
+-    spades_cmd = ['spades.py', '-o', out_dir, '--only-assembler', '-k', '21,41,61,81']
++    spades_cmd = ['spades', '-o', out_dir, '--only-assembler', '-k', '21,41,61,81']
+ 
+     if os.path.isfile(reads_1):
+         spades_cmd += ['-1', reads_1, '-2', reads_2]
+--- a/test/test_misc.py
++++ b/test/test_misc.py
+@@ -384,14 +384,14 @@ class TestMiscFunctions(unittest.TestCas
+ 
+     def test_spades_version_parsing_3(self):
+         spades_version_output = 'option -v not recognized\nSPAdes genome assembler v.3.5.0\n\n' \
+-                                'Usage: SPAdes-3.5.0-Darwin/bin/spades.py [options] ' \
++                                'Usage: SPAdes-3.5.0-Darwin/bin/spades [options] ' \
+                                 '-o <output_dir>\n\nBasic options:'
+         version = unicycler.misc.spades_version_from_spades_output(spades_version_output)
+         self.assertEqual(version, '3.5.0')
+ 
+     def test_spades_version_parsing_4(self):
+         spades_version_output = 'option -v not recognized\nSPAdes genome assembler v.2.4.0\n\n' \
+-                                'Usage: SPAdes-2.4.0-Darwin/bin/spades.py [options] ' \
++                                'Usage: SPAdes-2.4.0-Darwin/bin/spades [options] ' \
+                                 '-o <output_dir>\n\nBasic options:'
+         version = unicycler.misc.spades_version_from_spades_output(spades_version_output)
+         self.assertEqual(version, '2.4.0')
+--- a/README.md
++++ b/README.md
+@@ -93,7 +93,7 @@ Reasons to __not__ use Unicycler:
+     * [ICC](https://software.intel.com/en-us/c-compilers) also works (though I don't know the minimum required version number)
+ * [setuptools](https://packaging.python.org/installing/#install-pip-setuptools-and-wheel) (only required for installation of Unicycler)
+ * For short-read or hybrid assembly:
+-  * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 or later (`spades.py`)
++  * [SPAdes](http://bioinf.spbau.ru/spades) v3.6.2 or later (`spades`)
+ * For long-read or hybrid assembly:
+   * [Racon](https://github.com/isovic/racon) (`racon`)
+ * For polishing
+@@ -411,7 +411,7 @@ Run `unicycler --help_all` to see a comp
+ SPAdes assembly:
+   These options control the short-read SPAdes assembly at the beginning of the Unicycler pipeline.
+ 
+-  --spades_path SPADES_PATH           Path to the SPAdes executable (default: spades.py)
++  --spades_path SPADES_PATH           Path to the SPAdes executable (default: spades)
+   --no_correct                        Skip SPAdes error correction step (default: conduct SPAdes error
+                                       correction)
+   --min_kmer_frac MIN_KMER_FRAC       Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read
+--- a/setup.py
++++ b/setup.py
+@@ -63,7 +63,7 @@ def missing_tool(tool_name):
+ 
+ def tool_check():
+     # Check for required programs.
+-    tools = ['spades.py', 'java', 'pilon', 'samtools', 'bowtie2', 'bowtie2-build',
++    tools = ['spades', 'java', 'pilon', 'samtools', 'bowtie2', 'bowtie2-build',
+              'makeblastdb', 'tblastn']
+     missing_tools = []
+     for tool in tools:
+--- a/unicycler/misc.py
++++ b/unicycler/misc.py
+@@ -124,7 +124,7 @@ def check_spades(spades_path):
+ 
+     if not err.decode():
+         quit_with_error('SPAdes was found but does not produce output (make sure to use '
+-                        '"spades.py" location, not "spades")')
++                        '"spades" location, not "spades")')
+ 
+ 
+ def find_pilon(pilon_path, java_path, args):
+@@ -916,7 +916,7 @@ def spades_path_and_version(spades_path)
+ 
+ def spades_version_from_spades_output(spades_output):
+     """
+-    Parses the SPAdes version from the output of spades.py -v
++    Parses the SPAdes version from the output of spades -v
+     """
+     try:
+         return re.search(r'v(\d+\.\d+\.\d+)', spades_output).group(1)
+--- a/unicycler/unicycler.py
++++ b/unicycler/unicycler.py
+@@ -320,7 +320,7 @@ def get_arguments():
+                                              'These options control the short-read SPAdes '
+                                              'assembly at the beginning of the Unicycler pipeline.'
+                                              if show_all_args else argparse.SUPPRESS)
+-    spades_group.add_argument('--spades_path', type=str, default='spades.py',
++    spades_group.add_argument('--spades_path', type=str, default='spades',
+                               help='Path to the SPAdes executable'
+                                    if show_all_args else argparse.SUPPRESS)
+     spades_group.add_argument('--no_correct', action='store_true',
+@@ -753,7 +753,7 @@ def check_dependencies(args, short_reads
+         spades_path, spades_version, spades_status = '', '', 'not used'
+     else:
+         spades_path, spades_version, spades_status = spades_path_and_version(args.spades_path)
+-    spades_row = ['spades.py', spades_version, spades_status]
++    spades_row = ['spades', spades_version, spades_status]
+     if args.verbosity > 1:
+         spades_row.append(spades_path)
+     program_table.append(spades_row)
+@@ -861,7 +861,7 @@ def quit_if_dependency_problem(spades_st
+         quit_with_error('SPAdes cannot run due to an incompatible Python version')
+     if spades_status == 'bad':
+         quit_with_error('SPAdes was found but does not produce output (make sure to use '
+-                        '"spades.py" location, not "spades")')
++                        '"spades" location, not "spades")')
+     if makeblastdb_status == 'not found':
+         quit_with_error('could not find makeblastdb - either specify its location using '
+                         '--makeblastdb_path or use --no_rotate to remove BLAST dependency')

debian/rules

 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
 
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
+export PYBUILD_NAME=unicycler
 
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+# Build time tests are flaky
+export DH_BUILD_MAINT_OPTIONS=nocheck
 
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_clean:
 	echo "Avoid:  command 'UnicyclerClean' has no such option 'all'"
+	find . -name "*.o" -delete
+
+override_dh_auto_build:
+	dh_auto_build
+	# building the dynamic library requires extra make call
+	make
+
+override_dh_auto_test:
+	BUILDPATH=$(shell pybuild --print build_dir --interpreter python3) ; \
+	ln -s $(CURDIR)/sample_data $${BUILDPATH} ; \
+	cp -a unicycler/*.so $${BUILDPATH}/$(PYBUILD_NAME) ; \
+	PYTHONPATH=$${BUILDPATH}/$(PYBUILD_NAME) dh_auto_test