debian/changelog

+bcbio (1.1.2-2) unstable; urgency=medium
+
+  * Found Python3 incompatbility. Upstream has it already.
+
+ -- Steffen Moeller <moeller@debian.org>  Mon, 21 Jan 2019 23:56:26 +0100
+
 bcbio (1.1.2-1) unstable; urgency=medium
 
   * Initial release (Closes: #903386)

debian/control

@@ -31,8 +31,8 @@ Package: python3-bcbio
 Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends},
-         python3-seqcluster,
          python3-tornado
+Recommends: python3-seqcluster
 Description: library for analysing high-throughput sequencing data
  This package installs the Python 3 libraries of the bcbio-nextgen
  toolkit implementing best-practice pipelines for fully automated high

debian/patches/python3.patch

+Index: bcbio/bcbio/qc/contamination.py
+===================================================================
+--- bcbio.orig/bcbio/qc/contamination.py
++++ bcbio/bcbio/qc/contamination.py
+@@ -39,7 +39,7 @@ def _generate_estimates(bam_file, out_ba
+         cmd += _get_input_args(bam_file, data, out_base, background)
+         try:
+             do.run(cmd, "VerifyBamID contamination checks")
+-        except subprocess.CalledProcessError, msg:
++        except subprocess.CalledProcessError as msg:
+             def allowed_errors(l):
+                 return (l.find("Insufficient Available markers") >= 0 or
+                         l.find("No reads found in any of the regions") >= 0)

debian/patches/series

+python3.patch