Add a new metadata type of Metadata Files.

These are now used to store the list of chromosomes for species as well as the index for MAF files.

MAF tools have been enhanced to make use of index files when available.

TODO: When datasets are purged from disk, these files should also be purged.

tools/data_source/data_source.py

@@ -2,7 +2,8 @@
 #Retreives data from UCSC and stores in a file. UCSC parameters are provided in the input/output file.
 import urllib, sys, os, gzip, tempfile, shutil
 from galaxy import eggs
-from galaxy.datatypes import data
+#from galaxy.datatypes import data
+from galaxy.util import gzip_magic
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
@@ -14,7 +15,7 @@ def check_gzip( filename ):
     temp = open( filename, "U" )
     magic_check = temp.read( 2 )
     temp.close()
-    if magic_check != data.gzip_magic:
+    if magic_check != gzip_magic:
         return False
     return True