Merge pull request maximilianh#186 from kriemo/dataroot

add environment variable option (CBDATAROOT) to define dataRoot

docs/collections.rst

@@ -21,6 +21,10 @@ Add a statement like the following to your ``~/.cellbrowser.conf``::
 
     dataRoot='/celldata/'
 
+Alternatively, ``dataRoot`` can be set using the ``CBDATAROOT`` environment variable::
+
+    export CBDATAROOT='/celldata/'
+
 Then, create a "stub" cellbrowser.conf into this directory, it should only contain
 a single line like ``shortLabel="some description"``. 
 You can describe your collection as discussed under the **Describing

src/cbPyLib/cellbrowser/cellbrowser.py

@@ -4153,10 +4153,17 @@ def rebuildCollections(dataRoot, webRoot, collList):
         writeJson(collInfo, collOutFname)
 
 def findRoot(inDir=None):
-    " return directory dataRoot defined in config file "
-    dataRoot = getConfig("dataRoot")
+    """ return directory dataRoot defined in config file or CBDATAROOT
+    environment variable.
+    """
+
+    if 'CBDATAROOT' in os.environ:
+        dataRoot = os.environ['CBDATAROOT']
+    else:
+        dataRoot = getConfig("dataRoot")
+
     if dataRoot is None:
-        logging.info("dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported.")
+        logging.info("dataRoot is not set in ~/.cellbrowser.conf or via $CBDATAROOT. Dataset hierarchies are not supported.")
         return None
 
     dataRoot = abspath(expanduser(dataRoot).rstrip("/"))