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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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