Steffen Möller pushed to branch master at Debian Med / sepp
Commits: 5fd4cab3 by Steffen Moeller at 2020-12-12T23:29:25+01:00 Further refinement - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/using_python3_interpreter.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,7 +1,8 @@ -sepp (4.3.10+dfsg-4) UNRELEASED; urgency=medium +sepp (4.3.10+dfsg-4) unstable; urgency=medium * Team upload. * Now truly also bringing d/sepp.install to salsa + * d/rules clean: Allowing for repeated builds cleaning *.jar *.class -- Steffen Moeller <[email protected]> Sat, 12 Dec 2020 19:39:54 +0100 ===================================== debian/control ===================================== @@ -9,12 +9,12 @@ Build-Depends: debhelper-compat (= 13), python3, python3-setuptools, python3-dendropy, - pplacer, - hmmer, ant, libjenkins-json-java, libgoogle-gson-java, - ncbi-blast+ + ncbi-blast+ <!nocheck>, + pplacer <!nocheck>, + hmmer <!nocheck> Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/sepp Vcs-Git: https://salsa.debian.org/med-team/sepp.git ===================================== debian/patches/using_python3_interpreter.patch ===================================== @@ -5,43 +5,73 @@ Origin: https://www.debian.org/doc/packaging-manuals/python-policy/programs.html Forwarded: https://github.com/smirarab/sepp/issues/88 Last-Update: 2020-10-07 ---- a/run_abundance.py -+++ b/run_abundance.py +Index: sepp/run_abundance.py +=================================================================== +--- sepp.orig/run_abundance.py ++++ sepp/run_abundance.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.metagenomics import main ---- a/run_sepp.py -+++ b/run_sepp.py +Index: sepp/run_sepp.py +=================================================================== +--- sepp.orig/run_sepp.py ++++ sepp/run_sepp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive import ExhaustiveAlgorithm ---- a/run_tipp.py -+++ b/run_tipp.py +Index: sepp/run_tipp.py +=================================================================== +--- sepp.orig/run_tipp.py ++++ sepp/run_tipp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive_tipp import main ---- a/run_tipp_tool.py -+++ b/run_tipp_tool.py +Index: sepp/run_tipp_tool.py +=================================================================== +--- sepp.orig/run_tipp_tool.py ++++ sepp/run_tipp_tool.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- ---- a/run_upp.py -+++ b/run_upp.py +Index: sepp/run_upp.py +=================================================================== +--- sepp.orig/run_upp.py ++++ sepp/run_upp.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 # -*- coding: utf-8 -*- from sepp.exhaustive_upp import main +Index: sepp/sepp-package/run-sepp.sh +=================================================================== +--- sepp.orig/sepp-package/run-sepp.sh ++++ sepp/sepp-package/run-sepp.sh +@@ -134,7 +134,14 @@ set -e + if [ ! -z "$printDebug" ]; then + export SEPP_DEBUG=True + fi; +-python $DIR/sepp/run_sepp.py -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log ++ ++runMe=/usr/bin/run_sepp.py ++if [ -e $DIR/sepp/run_sepp.py ]; then ++ runMe=$DIR/sepp/run_sepp.py ++fi ++ ++echo "I: Invoking python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log" ++python3 $runMe -P $p -A $a -t $t -a $alg -r $rxi -f $f -o $name $opts -d $tmp/ -p $tmpssd 1>sepp-$name-out.log 2>sepp-$name-err.log + + tail sepp-$name-* + ===================================== debian/rules ===================================== @@ -38,6 +38,10 @@ override_dh_auto_clean: $(RM) -rf tools/bundled $(RM) -rf tools/merge/build $(RM) sepp.config tipp.config upp.config + find . -name "*.class" -delete + find . -name "*.jar" -delete + rm -f home.path sepp.egg-info/PKG-INFO sepp.egg-info/SOURCES.txt sepp.egg-info/dependency_links.txt sepp.egg-info/requires.txt sepp.egg-info/top_level.txt + override_dh_auto_install: dh_auto_install View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503 -- View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/5fd4cab3e7c8a096cb4b631b60916b75eddc0503 You're receiving this email because of your account on salsa.debian.org.
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