Sascha Steinbiss pushed to branch master at Debian Med / snp-sites
Commits: 3c28879a by Sascha Steinbiss at 2018-06-15T00:15:42+02:00 remove obsolete autotools deps - - - - - 457ee199 by Sascha Steinbiss at 2018-06-15T00:16:09+02:00 bump Standards-Version - - - - - 01442663 by Sascha Steinbiss at 2018-06-15T00:16:34+02:00 dh 11 - - - - - 6b0dcdc3 by Sascha Steinbiss at 2018-06-15T00:16:56+02:00 use secure copyright format URL - - - - - 9e1eb11b by Sascha Steinbiss at 2018-06-15T00:17:07+02:00 dch -r - - - - - 5d552ef5 by Sascha Steinbiss at 2018-06-15T00:17:24+02:00 remove obsolete Testsuite entry - - - - - 9f0e8daf by Sascha Steinbiss at 2018-06-15T00:17:36+02:00 use Salsa VCS-* - - - - - 9e1a5fac by Sascha Steinbiss at 2018-06-15T00:17:51+02:00 remove obsolete patches - - - - - ed8450d2 by Sascha Steinbiss at 2018-06-15T00:18:42+02:00 fix file modes - - - - - 17 changed files: - debian/changelog - debian/compat - debian/control - debian/copyright - debian/docs - debian/libsnp-sites1-dev.README.Debian - − debian/patches/add_lib_subunit.patch - − debian/patches/fix_manpage.patch - − debian/patches/reproducible-build.patch - − debian/patches/series - debian/snp-sites.README.Debian - debian/snp-sites.install - debian/snp-sites.manpages - debian/tests/alignment_file_one_line_per_sequence.aln.gz - debian/tests/build-lib - debian/tests/control - debian/watch Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,12 @@ -snp-sites (2.4.0-1) UNRELEASED; urgency=medium +snp-sites (2.4.0-1) unstable; urgency=medium * New upstream version. * Adjust watchfile to allow 'v' in version tags. * Update upstream metadata (thanks Steffen Moeller). + * Remove obsolete autotools Build-Depends. + * Use debhelper 11. + * Bump Standards-Version. + * Use secure copyright format URL. -- Sascha Steinbiss <[email protected]> Thu, 14 Jun 2018 17:29:53 +0200 ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -9 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -5,18 +5,15 @@ Uploaders: Jorge Soares <[email protected]>, Sascha Steinbiss <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 9.0.0), - autotools-dev, +Build-Depends: debhelper (>= 11), zlib1g-dev, check, pkg-config, - dh-autoreconf, d-shlibs, asciidoctor -Standards-Version: 3.9.8 -Testsuite: autopkgtest -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snp-sites.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/snp-sites.git +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/med-team/snp-sites +Vcs-Git: https://salsa.debian.org/med-team/snp-sites.git Homepage: https://github.com/sanger-pathogens/snp-sites Package: snp-sites ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: snp-sites Source: https://github.com/sanger-pathogens/snp-sites ===================================== debian/docs ===================================== ===================================== debian/libsnp-sites1-dev.README.Debian ===================================== ===================================== debian/patches/add_lib_subunit.patch deleted ===================================== --- a/debian/patches/add_lib_subunit.patch +++ /dev/null @@ -1,5 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 16 Sep 2015 15:08:04 +0200 -Bug-Debian: http://bugs.debian.org/799164 -Description: Add missing lib subunit - ===================================== debian/patches/fix_manpage.patch deleted ===================================== --- a/debian/patches/fix_manpage.patch +++ /dev/null @@ -1,86 +0,0 @@ -Description: Fix manpage -Author: Sascha Steinbiss <[email protected]> -Forwarded: https://github.com/sanger-pathogens/snp-sites/pull/47 -Applied-Upstream: v2.2.1 ---- a/snp-sites.txt -+++ b/snp-sites.txt -@@ -1,5 +1,5 @@ --SNP-SITESDOC(1) --============== -+SNP-SITES(1) -+============ - :doctype: manpage - - -@@ -15,10 +15,15 @@ - ----------- - This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats: - --a multi fasta alignment, VCF, relaxed phylip format. -+ - multi fasta alignment -+ - VCF -+ - relaxed phylip format - - OPTIONS - ------- -+*-r*:: -+ Output internal pseudo reference sequence -+ - *-m*:: - Output a multi fasta alignment file (default) - -@@ -32,16 +37,18 @@ - Specify an output filename - - *-h*:: -- This document -+ Show help message - - *-V*:: - Show version and exit - -+ - EXAMPLES - -------- --snp-sites my-alignment.aln - --snp-sites my-gzipped-alignment.aln.gz -+ snp-sites my-alignment.aln -+ -+ snp-sites my-gzipped-alignment.aln.gz - - - FORMAT OF THE INPUT FILE -@@ -49,12 +56,12 @@ - - Input files should look like this: - -->reference_sequence --aaccggtt -->comparison_sequence --AACCGGTT -->another_comparison_sequence --AACCGCTT -+ >reference_sequence -+ aaccggtt -+ >comparison_sequence -+ AACCGGTT -+ >another_comparison_sequence -+ AACCGCTT - - For more examples, visit: - https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data -@@ -63,6 +70,13 @@ - ------ - snp-sites was originally written by Andrew Page ([email protected]) - -+CITATION -+-------- -+If you use this program, please cite: -+"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", -+Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016), -+bioRxiv doi: http://dx.doi.org/10.1101/038190 -+ - COPYING - ------- - Wellcome Trust Sanger Institute Copyright (C) 2013 Wellcome Trust Sanger Institute ===================================== debian/patches/reproducible-build.patch deleted ===================================== --- a/debian/patches/reproducible-build.patch +++ /dev/null @@ -1,12 +0,0 @@ -Description: Manually set the timestamp in the manpage to the last modification time - ---- a/snp-sites.txt -+++ b/snp-sites.txt -@@ -1,6 +1,7 @@ - SNP-SITES(1) - ============ - :doctype: manpage -+:revdate: 2015-09-03 - - - NAME ===================================== debian/patches/series deleted ===================================== --- a/debian/patches/series +++ /dev/null ===================================== debian/snp-sites.README.Debian ===================================== ===================================== debian/snp-sites.install ===================================== --- a/debian/snp-sites.install +++ b/debian/snp-sites.install @@ -1 +1 @@ -usr/bin/snp-sites \ No newline at end of file +usr/bin/snp-sites ===================================== debian/snp-sites.manpages ===================================== ===================================== debian/tests/alignment_file_one_line_per_sequence.aln.gz ===================================== Binary files a/debian/tests/alignment_file_one_line_per_sequence.aln.gz and b/debian/tests/alignment_file_one_line_per_sequence.aln.gz differ ===================================== debian/tests/build-lib ===================================== ===================================== debian/tests/control ===================================== ===================================== debian/watch ===================================== View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ab456e4206b714976b368b75469c6d6d3d1026ef...ed8450d20becfd99a99af382674140ff962f5816 -- View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ab456e4206b714976b368b75469c6d6d3d1026ef...ed8450d20becfd99a99af382674140ff962f5816 You're receiving this email because of your account on salsa.debian.org.
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