should #fix 30

Snakefile

@@ -4,6 +4,7 @@ import gzip
 import json
 import bz2
 from copy import deepcopy
+import subprocess
 
 
 def dict_merge(a, b):
@@ -82,6 +83,27 @@ def prepare_environment(stepname):
     return out, os.path.join(out, '%s.log' % stepname)
 
 
+def symlink_prokka():
+    # ## prokka by default will look databases where is located the binary.
+    # ## we have to softlink to put the binary somewhere and the databases somewhere else.
+    cmd = """
+    if [[ "{DBPATH}" = /* ]]
+    then
+        PP={DBPATH};
+    else
+        PP=$PWD/{DBPATH};
+    fi
+    DD=$(dirname $(which prokka))/../db
+    if [[ ! -L $DD ]]
+    then
+        echo "Softlinking $DD to $PP"
+        cd $(dirname $(which prokka))/.. && ln -s $PP db
+    fi
+    """
+    shell(cmd)
+
+symlink_prokka()
+
 # INCLUDES RULES
 include:
     "rules/Util.rules"

rules/Util.rules

@@ -55,6 +55,7 @@ rule _DOWNLOAD_PROKKA_DATABASES:
         """
 
 
+
 rule _DOWNLOAD_TRIMMOMATIC_ADAPTERS:
     output:
         "{DBPATH}/adapters/adapters.done"