Add a patch to fix installing step

Author: Liubov Chuprikova <chuprikovalv@gmail.com>

Last-Update: Fri, 7 September 2018 18:46:31 +0200

Description: Skip extra steps (make distclean and make) while installing as

they were done earlier

--- a/setup.py

+++ b/setup.py

@@ -99,21 +99,21 @@

                 sys.exit('Error: no write permission for ' + self.install_scripts + '  ' +

                          'Perhaps you need to use sudo?')

-            # Clean up any previous Unicycler compilation.

-            clean_cmd = ['make', 'distclean']

-            self.execute(lambda: subprocess.call(clean_cmd), [],

-                         'Cleaning previous compilation: ' + ' '.join(clean_cmd))

-

-            # Build Unicycler's C++ code.

-            make_cmd = ['make']

-            try:

-                make_cmd += ['-j', str(min(8, multiprocessing.cpu_count()))]

-            except NotImplementedError:

-                pass

-            if self.makeargs:

-                make_cmd += shlex.split(self.makeargs)

-            self.execute(lambda: subprocess.call(make_cmd), [],

-                         'Compiling Unicycler: ' + ' '.join(make_cmd))

+#            # Clean up any previous Unicycler compilation.

+#            clean_cmd = ['make', 'distclean']

+#            self.execute(lambda: subprocess.call(clean_cmd), [],

+#                         'Cleaning previous compilation: ' + ' '.join(clean_cmd))

+#

+#            # Build Unicycler's C++ code.

+#            make_cmd = ['make']

+#            try:

+#                make_cmd += ['-j', str(min(8, multiprocessing.cpu_count()))]

+#            except NotImplementedError:

+#                pass

+#            if self.makeargs:

+#                make_cmd += shlex.split(self.makeargs)

+#            self.execute(lambda: subprocess.call(make_cmd), [],

+#                         'Compiling Unicycler: ' + ' '.join(make_cmd))

             cpp_code = os.path.join('unicycler', 'cpp_functions.so')

             if not os.path.isfile(cpp_code):

                 sys.exit("Error: compilation of Unicycler's C++ component failed")

spades.patch

# bowtie.patch 

install_wo_extra_steps.patch