[med-svn] [Git][med-team/bcbio][master] 2 commits: Fixed Python3 incompatibility

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
9dfe1f42 by Steffen Möller at 2019-01-21T22:57:04Z
Fixed Python3 incompatibility

- - - - -
22a63cd0 by Steffen Möller at 2019-01-22T10:48:20Z
Demoted seqcluster as 'recommended'

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/python3.patch
- + debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+bcbio (1.1.2-2) unstable; urgency=medium
+
+  * Found Python3 incompatbility. Upstream has it already.
+
+ -- Steffen Moeller <moeller at 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
=====================================
@@ -0,0 +1,13 @@
+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
=====================================
@@ -0,0 +1 @@
+python3.patch



View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd...22a63cd0c73b96fb883956896e602494eb9d2719
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