Andreas Tille pushed to branch master at Debian Med / rsem
Commits: ec10db04 by Andreas Tille at 2018-02-18T20:28:25+01:00 DEP3 - - - - - 2d292817 by Andreas Tille at 2018-02-18T20:30:00+01:00 Remove samtools mentioning from d/copyright - - - - - 74dd92d3 by Andreas Tille at 2018-02-18T20:33:39+01:00 cme fix dpkg-control - - - - - da59abab by Andreas Tille at 2018-02-18T20:34:31+01:00 debhelper 11 - - - - - b85e15d2 by Andreas Tille at 2018-02-18T21:01:53+01:00 Remove unused --parallel - - - - - a430e852 by Andreas Tille at 2018-02-18T21:04:48+01:00 do not parse d/changelog; upload to experimental - - - - - 6 changed files: - debian/changelog - debian/compat - debian/control - debian/copyright - debian/patches/use_debian_packaged_samtools.patch - debian/rules Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,12 +1,15 @@ -rsem (1.3.0+dfsg-1) UNRELEASED; urgency=medium +rsem (1.3.0+dfsg-1) experimental; urgency=medium * New upstream version * d/watch: - version=4 - xz compression * remove code copy of samtools-1.3 + * cme fix dpkg-control + * debhelper 11 + * d/rules: do not parse d/changelog - -- Andreas Tille <ti...@debian.org> Fri, 09 Dec 2016 14:26:08 +0100 + -- Andreas Tille <ti...@debian.org> Sun, 18 Feb 2018 20:34:37 +0100 rsem (1.2.31+dfsg-1) unstable; urgency=medium ===================================== debian/compat ===================================== --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -9 +11 ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian. Uploaders: Michael R. Crusoe <michael.cru...@gmail.com>, Andreas Tille <ti...@debian.org> Section: science -Priority: extra -Build-Depends: debhelper (>= 9), +Priority: optional +Build-Depends: debhelper (>= 11~), zlib1g-dev, libncurses5-dev, libboost-dev, @@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 9), # bowtie is a run-time dependency available on only a few systems, not actually # needed for building but it prevents the creation of uninstallable packages bowtie | bowtie2 -Standards-Version: 3.9.8 +Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git Homepage: http://deweylab.biostat.wisc.edu/rsem/ ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -30,45 +30,6 @@ License: GPL-3 On Debian systems, the full text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'. -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz - -Files: samtools-1.3/* -Copyright: © 2008–2016, Genome Research Ltd. (GRL) - © 2003–2006, 2008–2011, by Heng Li <lh3...@live.co.uk> - © 2009–2012 Broad Institute - © 2010 Illumina, Inc. - © 2012–2013 Peter Cock, The James Hutton Institute. -License: MIT -Comment: Modified version of samtools included as per upstream - -Files: samtools-1.3/win32/xcurses.h -Copyright: Public Domain -License: public-domain - This file is part of PDCurses (http://pdcurses.sourceforge.net/), - which is in the public domain. - -Files: samtools-1.3/win32/z*.h -Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler -License: zlib - This software is provided 'as-is', without any express or implied - warranty. In no event will the authors be held liable for any damages - arising from the use of this software. - . - Permission is granted to anyone to use this software for any purpose, - including commercial applications, and to alter it and redistribute it - freely, subject to the following restrictions: - . - 1. The origin of this software must not be misrepresented; you must not - claim that you wrote the original software. If you use this software - in a product, an acknowledgment in the product documentation would be - appreciated but is not required. - 2. Altered source versions must be plainly marked as such, and must not be - misrepresented as being the original software. - 3. This notice may not be removed or altered from any source distribution. - . - Jean-loup Gailly Mark Adler - jl...@gzip.org mad...@alumni.caltech.edu License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy @@ -88,4 +49,3 @@ License: MIT LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - ===================================== debian/patches/use_debian_packaged_samtools.patch ===================================== --- a/debian/patches/use_debian_packaged_samtools.patch +++ b/debian/patches/use_debian_packaged_samtools.patch @@ -1,3 +1,7 @@ +Author: Andreas Tille <ti...@debian.org> +Last-Update: Fri, 09 Dec 2016 14:26:08 +0100 +Description: Use Debian packaged samtools + --- a/Makefile +++ b/Makefile @@ -12,7 +12,7 @@ BOOST = . ===================================== debian/rules ===================================== --- a/debian/rules +++ b/debian/rules @@ -2,13 +2,12 @@ DH_VERBOSE := 1 -DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') -VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +include /usr/share/dpkg/default.mk export DEB_BUILD_MAINT_OPTIONS=hardening=+all %: - dh $@ --parallel + dh $@ override_dh_auto_build: dh_auto_build -- BOOST=/usr/include prefix=debian/tmp @@ -16,13 +15,13 @@ override_dh_auto_build: rsem-control-fdr rsem-generate-ngvector \ rsem-plot-transcript-wiggles rsem-prepare-reference \ rsem-run-ebseq; do pod2man $${prog} debian/$${prog}.1; done - help2man ./rsem-gff3-to-gtf --no-info --version-string="${VERSION}" \ + help2man ./rsem-gff3-to-gtf --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ --name 'Convert GFF3 files to GTF files.' > \ debian/rsem-gff3-to-gtf.1 - help2man ./rsem-bam2wig --no-info --version-string="${VERSION}" \ + help2man ./rsem-bam2wig --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ --name 'Convert BAM files to wiggle files.' > \ debian/rsem-bam2wig.1 - help2man ./rsem-simulate-reads --no-info --version-string="${VERSION}" \ + help2man ./rsem-simulate-reads --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ debian/rsem-simulate-reads.1 View it on GitLab: https://salsa.debian.org/med-team/rsem/compare/a4dd6340bfb01579d6ca796db6816ce2294a6b8c...a430e8521ecd3f9b9f9c6c8962054d43594d66b6 --- View it on GitLab: https://salsa.debian.org/med-team/rsem/compare/a4dd6340bfb01579d6ca796db6816ce2294a6b8c...a430e8521ecd3f9b9f9c6c8962054d43594d66b6 You're receiving this email because of your account on salsa.debian.org.
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