Version increment, fix pplacer issue

Author: pchaumeil

docs/src/changelog.rst

@@ -2,6 +2,14 @@
 Change log
 ==========
 
+2.2.2
+-----
+
+Bug Fixes:
+
+* Fix Pplacer issue
+
+
 2.2.1
 -----
 

gtdbtk/__init__.py

@@ -29,4 +29,4 @@
 __status__ = 'Production'
 __title__ = 'GTDB-Tk'
 __url__ = 'https://github.com/Ecogenomics/GTDBTk'
-__version__ = '2.2.1'
+__version__ = '2.2.2'

gtdbtk/classify.py

@@ -263,7 +263,7 @@ def place_genomes(self,
         if levelopt is None or levelopt == 'high':
             self.logger.info(f'pplacer version: {pplacer.version}')
         # #DEBUG: Skip pplacer
-        run_pplacer = False
+        run_pplacer = True
         if run_pplacer:
             pplacer.run(self.pplacer_cpus, 'wag', pplacer_ref_pkg, pplacer_json_out,
                         user_msa_file, pplacer_out, pplacer_mmap_file)

gtdbtk/main.py

@@ -492,7 +492,7 @@ def run_test(self, options):
 
             shutil.copytree(input_dir, genome_test_dir)
 
-            args = ['gtdbtk', 'classify_wf', '--genome_dir', genome_test_dir,
+            args = ['gtdbtk', 'classify_wf','--skip_ani_screen', '--genome_dir', genome_test_dir,
                     '--out_dir', output_dir, '--cpus', str(options.cpus), '-f']
             self.logger.info('Command: {}'.format(' '.join(args)))