Stuart Prescott pushed to branch master at Debian Med / tvc
Commits: bc168444 by Stuart Prescott at 2020-03-01T16:07:31+11:00 Use Python 3 in package - - - - - d9b250b7 by Stuart Prescott at 2020-03-01T16:07:31+11:00 Update S-V to 4.5.0 - - - - - e0c907d9 by Stuart Prescott at 2020-03-01T16:07:31+11:00 Switch to debhelper-compat (= 12) - - - - - 634b53df by Stuart Prescott at 2020-03-01T16:07:31+11:00 Add R3: no - - - - - 67c05a77 by Stuart Prescott at 2020-03-01T16:07:51+11:00 Add changelog for upload - - - - - 5 changed files: - debian/changelog - − debian/compat - debian/control - + debian/patches/python3.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +tvc (5.0.3+git20151221.80e144e+dfsg-3) unstable; urgency=medium + + * Team upload. + * Use Python 3 in scripts (Closes: #945720). + * Add Rules-Requires-Root: no. + * Update Standards-Version to 4.5.0 (no changes required). + * Switch to debhelper-compat (= 12). + + -- Stuart Prescott <[email protected]> Sun, 01 Mar 2020 15:57:45 +1100 + tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium [ Logan Rosen ] ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -4,23 +4,24 @@ Uploaders: Dominique Belhachemi <[email protected]>, Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev -Standards-Version: 4.2.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Homepage: http://ioncommunity.thermofisher.com +Rules-Requires-Root: no Package: tvc Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, - python + python3 Description: genetic variant caller for Ion Torrent sequencing platforms Torrent Variant Caller (TVC) is a genetic variant caller for Ion Torrent sequencing platforms, and is specially optimized to exploit the ===================================== debian/patches/python3.patch ===================================== @@ -0,0 +1,45 @@ +--- a/bin/variant_caller_pipeline.py ++++ b/bin/variant_caller_pipeline.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/python3 + # Copyright (C) 2011 Ion Torrent Systems, Inc. All Rights Reserved + + import sys +@@ -12,7 +12,7 @@ + def printtime(message, *args): + if args: + message = message % args +- print "[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message ++ print("[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message) + sys.stdout.flush() + sys.stderr.flush() + +@@ -133,7 +133,7 @@ + json_file = open(options.paramfile, 'r') + parameters = json.load(json_file) + json_file.close() +- if parameters.has_key('pluginconfig'): ++ if 'pluginconfig' in parameters: + parameters = parameters['pluginconfig'] + except: + printtime('ERROR: No parameter file found at: ' + options.paramfile) +--- a/external/vcflib/multichoose/multipermute.py ++++ b/external/vcflib/multichoose/multipermute.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/python3 + # -*- coding: utf-8 -*- + # multipermute.py - permutations of a multiset + # Erik Garrison <[email protected]> 2010 +@@ -92,7 +92,7 @@ + if multiset != []: + for permutation in permutations(multiset): + for item in permutation: +- print item, +- print ++ print(item, end=" ") ++ print() + else: +- print "usage", sys.argv[0], "<multiset>" ++ print("usage", sys.argv[0], "<multiset>") ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ hurd.patch sse.patch use_debian_packaged_smithwaterman.patch # use_debian_packaged_vcflib.patch +python3.patch View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35 -- View it on GitLab: https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35 You're receiving this email because of your account on salsa.debian.org.
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