Version increment, fix pplacer issue

Ecogenomics · Feb 14, 2023 · 95b1358 · 95b1358
1 parent 45bbba9
commit 95b1358
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git a/docs/src/changelog.rst b/docs/src/changelog.rst
@@ -2,6 +2,14 @@
 Change log
 ==========
 
+2.2.2
+-----
+
+Bug Fixes:
+
+* Fix Pplacer issue
+
+
 2.2.1
 -----
 

diff --git a/gtdbtk/__init__.py b/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'
diff --git a/gtdbtk/classify.py b/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)

diff --git a/gtdbtk/main.py b/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)))