v0.1.4: fix remote CWL builds with vcfanno inputs

Make use of specific configuration (versus filesystem) keys in
general input files.

New release also includes python3 fixes.

bcbiovm/arvados/retriever.py

@@ -158,6 +158,8 @@ def add_remotes(items, config):
     """
     if config.get(KEY):
         config = config[KEY]
+    elif config.get(CONFIG_KEY):
+        config = config[CONFIG_KEY]
     find_fn = _find_file(config)
     return sret.fill_remote(items, find_fn, _is_remote)
 

bcbiovm/dnanexus/retriever.py

@@ -187,6 +187,8 @@ def add_remotes(items, config):
     """
     if config.get(KEY):
         config = config[KEY]
+    elif config.get(CONFIG_KEY):
+        config = config[CONFIG_KEY]
     find_fn = _find_file(config)
     return sret.fill_remote(items, find_fn, _is_remote)
 

bcbiovm/sbgenomics/retriever.py

@@ -156,6 +156,8 @@ def add_remotes(items, config):
     """
     if config.get(KEY):
         config = config[KEY]
+    elif config.get(CONFIG_KEY):
+        config = config[CONFIG_KEY]
     find_fn = _find_file(config)
     return sret.fill_remote(items, find_fn, _is_remote)
 

setup.py

@@ -4,7 +4,7 @@
 import sys
 from setuptools import setup, find_packages
 
-version = "0.1.3"
+version = "0.1.4"
 
 def write_version_py():
     version_py = os.path.join(os.path.dirname(__file__), "bcbiovm", "version.py")