This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository r8s.
commit 4d1f06a7dd7a9b94d9560413c0054356aecd2444 Author: Andreas Tille <[email protected]> Date: Tue Jun 23 17:41:38 2015 +0200 Add initial Debian packaging --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 40 ++++++++++++++++++++++++++++++++++++++++ debian/copyright | 11 +++++++++++ debian/get-orig-source | 29 +++++++++++++++++++++++++++++ debian/rules | 23 +++++++++++++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++++ debian/watch | 3 +++ 9 files changed, 125 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..0781d86 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +r8s (1.8+ds-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- DMPT <[email protected]> Tue, 23 Jun 2015 17:33:18 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..4324d94 --- /dev/null +++ b/debian/control @@ -0,0 +1,40 @@ +Source: r8s +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/r8s.git +Vcs-Git: git://anonscm.debian.org/debian-med/r8s.git +Homepage: http://loco.biosci.arizona.edu/r8s/ + +Package: r8s +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: Analysis of rates ("r8s") of evolution + This is a program for estimating absolute rates ("r8s") of molecular + evolution and divergence times on a phylogenetic tree. It implements + several methods for estimating these parameters ranging from fairly + standard maximum likelihood methods in the context of global or local + molecular clocks to more experimental semiparametric and nonparametric + methods that relax the stringency of the clock assumption using + smoothing methods. Its starting point is a given phylogenetic tree and a + given set of estimated branch lengths (numbers of substitutions along + each branch). In addition one or more calibration points can be added to + permit scaling of rates and times to real units. These calibrations can + take one of two forms: assignment of a fixed age to a node, or + enforcement of a minimum or maximum age constraint on a node, which is + generally a better reflection of the information content of fossil + evidence. Terminal nodes are permitted to occur at any point in time, + allowing investigation of rate variation in phylogenies such as those + obtained from "serial" samples of viral lineages through time. Finally, + it is possible to assign all divergence times (perhaps based on outside + estimates of divergence times) and examine molecular rate variation + under several models of smoothing. + . + This version contains ancestral state reconstruction and model testing + for several markov models of morphological evolution. + . + The program reads "NEXUS" formatted data files. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..c76e73d --- /dev/null +++ b/debian/copyright @@ -0,0 +1,11 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: © 2014 maintainername <[email protected]> +License: <license> diff --git a/debian/get-orig-source b/debian/get-orig-source new file mode 100755 index 0000000..1dc497d --- /dev/null +++ b/debian/get-orig-source @@ -0,0 +1,29 @@ +#!/bin/sh + +COMPRESS=xz + +set -e + +NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` + +TARDIR=${NAME}-${VERSION} +mkdir -p ../tarballs +cd ../tarballs +# need to clean up the tarballs dir first because upstream tarball might +# contain a directory with unpredictable name +rm -rf * +wget http://loco.biosci.arizona.edu/r8s/${NAME}.dist.tgz +tar xaf ${NAME}.dist.tgz +mv dist ${TARDIR} +# remove binary +rm -f ${TARDIR}/r8s +# remove PDF without source +rm -f ${TARDIR}/r8s*.manual.pdf +# remove cruft +rm -f ${TARDIR}/*~ +# fix permissions +chmod 644 ${TARDIR}/nr*.[ch] + +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}" +rm -rf ${TARDIR} diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..58ec00b --- /dev/null +++ b/debian/rules @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# some helpful variables - uncomment them if needed +# shamelessly stolen from http://jmtd.net/log/awk/ +#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') +#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') +#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') +#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) +#GIT_TAG := $(subst ~,_,$(VERSION)) + +# alternatively to manually set those variables you can +# include /usr/share/cdbs/1/rules/buildvars.mk +# and use what is set there. Any hint whether dh might set variables in +# a similar manner are welcome. + +%: + dh $@ + +#get-orig-source: +# . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..0610270 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Michael J. Sanderson + Title: "r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock" + Journal: Bioinformatics + Year: 2003 + Volume: 19 + Number: 2 + Pages: 301-302 + DOI: 10.1093/bioinformatics/19.2.301 + PMID: 12538260 + URL: http://bioinformatics.oxfordjournals.org/content/19/2/301.abstract + eprint: http://bioinformatics.oxfordjournals.org/content/19/2/301.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..0237453 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +#version=3 +# No proper watch file possible to download from +# http://loco.biosci.arizona.edu/r8s/ \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r8s.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
