Andreas Tille pushed to branch master at Debian Med / discosnp
Commits: 45dc3905 by Andreas Tille at 2020-01-27T15:46:18+01:00 Do not tweak Python3 interpreter in d/rules once this was done properly in a patch - - - - - 38b49ece by Andreas Tille at 2020-01-27T15:52:34+01:00 Fix POSIX shell syntax - - - - - d74c1212 by Andreas Tille at 2020-01-27T15:53:16+01:00 discoSnpRAD is a dir with extra scripts - - - - - f56c821b by Andreas Tille at 2020-01-27T15:55:26+01:00 Adapt to new names - - - - - bbd033a4 by Andreas Tille at 2020-01-27T15:59:17+01:00 Fix autopkgtest - - - - - 30cd3f3d by Andreas Tille at 2020-01-27T16:02:05+01:00 Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/install - debian/lintian-overrides - debian/patches/series - + debian/patches/shell_syntax.patch - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -discosnp (2.4.3-1) UNRELEASED; urgency=medium +discosnp (2.4.3-1) unstable; urgency=medium [ Steffen Moeller ] * New upstream version @@ -13,7 +13,7 @@ discosnp (2.4.3-1) UNRELEASED; urgency=medium * Remove trailing whitespace in debian/changelog (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository. - -- Andreas Tille <[email protected]> Mon, 27 Jan 2020 14:14:13 +0100 + -- Andreas Tille <[email protected]> Mon, 27 Jan 2020 15:59:28 +0100 discosnp (2.3.0-3) unstable; urgency=medium ===================================== debian/install ===================================== @@ -1,3 +1,3 @@ scripts usr/share/discosnp +discoSnpRAD usr/share/discosnp run_discoSnp*.sh usr/bin -discoSnpRAD usr/bin ===================================== debian/lintian-overrides ===================================== @@ -1,5 +1,4 @@ # see https://lists.debian.org/debian-med/2018/06/msg00043.html -discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh -discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh +discosnp: script-with-language-extension usr/bin/run_*.sh # The doc is where it belongs to -discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/scripts_RAD/README.md +discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/*/README.md ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ spelling.patch #fix_scripts.patch adapt_test_scripts.patch 2to3.patch +shell_syntax.patch ===================================== debian/patches/shell_syntax.patch ===================================== @@ -0,0 +1,15 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Mon, 27 Jan 2020 15:51:58 +0100 +Description: Fix POSIX shell syntax + +--- a/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh ++++ b/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh +@@ -13,7 +13,7 @@ bold=`tput bold` + reset=`tput sgr0` + + +-function help { ++help() { + echo $reset + echo "=====================================================" + echo "Filtering, clustering per locus and vcf formatting of $rawdiscofile" ===================================== debian/rules ===================================== @@ -15,9 +15,6 @@ override_dh_install: mv debian/$(DEB_SOURCE)/usr/bin/read_file_names debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin rm -rf debian/$(DEB_SOURCE)/usr/share/discosnp/scripts/jenkins - for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \ - sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \ - done override_dh_installman: dh_installman ===================================== debian/tests/run-unit-test ===================================== @@ -11,7 +11,7 @@ fi cp -a /usr/share/doc/${pkg}/test/* $AUTOPKGTEST_TMP cd $AUTOPKGTEST_TMP -gunzip ref_discoRes_k_31_c_auto_D_100_P_1_b_0_coherent*.gz +gunzip ref_*.fa.gz chmod +x simple_test.sh ./simple_test.sh View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6 -- View it on GitLab: https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6 You're receiving this email because of your account on salsa.debian.org.
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