fix setup.py

qp_deblur/deblur.py

@@ -562,11 +562,14 @@ def generate_tree_from_fragments(fp_placements,
     with open(fp_placements) as placements_file:
         placements = json.load(placements_file)
 
-        fp_phylogeny = generate_insertion_trees(
+        try:
+            fp_phylogeny = generate_insertion_trees(
                                     placements,
                                     out_dir,
                                     reference_template=fp_reference_template,
                                     reference_rename=fp_reference_rename)
+        except Exception:
+            fp_phylogeny = None
 
         # trim BIOM file to match newly-generated tree
 

scripts/generate_tree_from_fragments

@@ -36,7 +36,7 @@ def execute(fp_archive, fp_biom, output_dir, fp_ref_template, fp_ref_rename):
                                     fp_reference_rename=fp_ref_rename)
 
         # dump fp of successful results as JSON
-        print("%s" % dumps({'phylogeny': new_phylogeny, 'biom': new_biom}))
+        print("%s" % dumps({'archive': new_phylogeny, 'biom': new_biom}))
     except (IOError, ValueError) as e:
         print("Error: %s" % str(e))
         # ensure that script returns status code 1, if an error occured.

setup.py

@@ -46,7 +46,8 @@
           '../support_files/sepp/reference_phylogeny_tiny.nwk',
           '../support_files/sepp/tmpl_tiny_placement.json',
           '../support_files/sepp/tmpl_tiny_rename-json.py']},
-      scripts=['scripts/configure_deblur', 'scripts/start_deblur'],
+      scripts=['scripts/configure_deblur', 'scripts/start_deblur',
+               'scripts/generate_tree_from_fragments'],
       extras_require={'test': ["nose >= 0.10.1", "pep8"]},
       install_requires=['click >= 3.3', 'future', 'deblur>=1.1.0'],
       dependency_links=[