Fixed a couple of messages in testing, fixed Daijin failing when DRMA…

…A is not present (EI-CoreBioinformatics#119), fixed requirements, added conda recipes
lucventurini · May 10, 2018 · 2fbe61b · 2fbe61b
1 parent c9e2e7e
commit 2fbe61b
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Showing 19 changed files with 534 additions and 281 deletions.
diff --git a/.circleci-TBA/config.yml b/.circleci-TBA/config.yml
diff --git a/Mikado/__init__.py b/Mikado/__init__.py
@@ -10,7 +10,7 @@
 __author__ = 'Luca Venturini'
 __license__ = 'GPL3'
 __copyright__ = 'Copyright 2015-2016 Luca Venturini'
-__version__ = "1.2"
+__version__ = "1.2.1"
 
 __all__ = ["configuration",
            "exceptions",

diff --git a/Mikado/daijin/__init__.py b/Mikado/daijin/__init__.py
@@ -330,7 +330,15 @@ def assemble_transcripts_pipeline(args):
 
     drmaa_var = None
     if args.no_drmaa is False and res_cmd:
-        drmaa_var = res_cmd
+        try:
+            import drmaa
+            _ = drmaa.Session()
+        except (RuntimeError,ImportError,AttributeError):
+            print("WARNING: DRMAA not installed or not configured properly. Switching to local/cluster mode. Please use the \"-nd\" flag to run Daijin if you do not plan to use DRMAA.", file=sys.stderr)
+            drmaa_var = None
+            args.no_drmaa = True
+        else:
+            drmaa_var = res_cmd
 
     if drmaa_var or cluster_var:
         if os.path.exists(args.hpc_conf):
@@ -425,7 +433,15 @@ def mikado_pipeline(args):
 
     drmaa_var = None
     if args.no_drmaa is False and res_cmd:
-        drmaa_var = res_cmd
+        try:
+            import drmaa
+            _ = drmaa.Session()
+        except (RuntimeError,ImportError,AttributeError):
+            print("WARNING: DRMAA not installed or not configured properly. Switching to local/cluster mode. Please use the \"-nd\" flag to run Daijin if you do not plan to use DRMAA.", file=sys.stderr)
+            drmaa_var = None
+            args.no_drmaa = True
+        else:
+            drmaa_var = res_cmd        
 
     if drmaa_var or cluster_var:
         if os.path.exists(args.hpc_conf):