snakemake zhuzhing

examples/snakefile

@@ -33,11 +33,12 @@ skip_tests = ["download_files",
 			  "jonr_1", #431
 			  "add_reports", #433
 			  "embedded_python_post_processing", #434
-			  "serialization_replace_genomes" #632
+			  "serialization_replace_genomes", #632
+              "migration_human_spatial_malaria_sim"
               ]
 
-# "migration_spatial_malaria_sim",	# needs vpn connection
-# "migration_spatial_vector_sim",	# needs vpn connection
+# "migration_human_spatial_malaria_sim",	# needs vpn connection
+
 
 for dir in dirs:
     if os.path.isdir( dir ) and str( dir ).startswith( "." ) == False and os.path.exists( dir + "/example.py" ):
@@ -213,11 +214,11 @@ rule diagnostic_survey:
         shell(get_command("diagnostic_survey", python_version=config['python_version']))
 
 
-rule migration_spatial_malaria_sim:
+rule migration_human_spatial_malaria_sim:
     input: 
     output: Path("migration_human_spatial_malaria_sim", "experiment_id")
     run:        
-        shell(get_command("migration_spatial_malaria_sim", python_version=config['python_version']))
+        shell(get_command("migration_human_spatial_malaria_sim", python_version=config['python_version']))
 
 rule add_reports:
     input: 
@@ -293,7 +294,7 @@ rule migration_vector_and_microsporidia:
     input:
     output: Path("migration_vector_and_microsporidia", "experiment_id")
     run:
-        shell(get_command("microsporidia", python_version=config['python_version']))
+        shell(get_command("migration_vector_and_microsporidia", python_version=config['python_version']))
 
 rule vector_surveillance:
     input: