[med-svn] [r8s] 02/06: Add initial Debian packaging
Andreas Tille
tille at debian.org
Tue Jun 23 16:02:44 UTC 2015
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 <tille at debian.org>
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 <debian-med-packaging at lists.alioth.debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <maintainer at e.mail>
+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
--
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