Adjust bx-python imports for https://github.com/bxlab/bx-python/commit/fd08da3b49e89e0accd2c372d4a99427628ce432

lib/galaxy/datatypes/util/maf_utilities.py

@@ -45,7 +45,7 @@ def src_split(src):
 def src_merge(spec, chrom, contig=None):
     if None in [spec, chrom]:
         spec = chrom = spec or chrom
-    return bx.align.maf.src_merge(spec, chrom, contig)
+    return bx.align.src_merge(spec, chrom, contig)
 
 
 def get_species_in_block(block):

tools/maf/maf_to_bed.py

@@ -9,6 +9,7 @@ import sys
 from collections import OrderedDict
 
 from bx.align import maf
+from bx.align.core import src_split
 
 
 def __main__():
@@ -28,7 +29,7 @@ def __main__():
         try:
             for i, m in enumerate(maf.Reader(open(input_filename, 'r'))):
                 for c in m.components:
-                    spec, chrom = maf.src_split(c.src)
+                    spec, chrom = src_split(c.src)
                     if not spec or not chrom:
                         spec = c.src
                     species[spec] = None
@@ -64,7 +65,7 @@ def __main__():
             if len(l) < num_species and partial == "partial_disallowed":
                 continue
             for c in l:
-                spec, chrom = maf.src_split(c.src)
+                spec, chrom = src_split(c.src)
                 if not spec or not chrom:
                     spec = chrom = c.src
                 if spec not in out_files.keys():

tools/maf/maf_to_bed.xml

@@ -1,4 +1,4 @@
-<tool id="MAF_To_BED1" name="MAF to BED" version="1.0.0">
+<tool id="MAF_To_BED1" name="MAF to BED" version="1.0.0" profile="16.04">
     <description>Converts a MAF formatted file to the BED format</description>
     <macros>
         <import>macros.xml</import>