[med-svn] r19437 - in trunk/packages: . hyphy hyphy/trunk hyphy/trunk/debian hyphy/trunk/debian/source hyphy/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Mon Jun 29 12:11:39 UTC 2015
Author: tille
Date: 2015-06-29 12:11:38 +0000 (Mon, 29 Jun 2015)
New Revision: 19437
Added:
trunk/packages/hyphy/
trunk/packages/hyphy/trunk/
trunk/packages/hyphy/trunk/debian/
trunk/packages/hyphy/trunk/debian/changelog
trunk/packages/hyphy/trunk/debian/compat
trunk/packages/hyphy/trunk/debian/control
trunk/packages/hyphy/trunk/debian/copyright
trunk/packages/hyphy/trunk/debian/rules
trunk/packages/hyphy/trunk/debian/source/
trunk/packages/hyphy/trunk/debian/source/format
trunk/packages/hyphy/trunk/debian/upstream/
trunk/packages/hyphy/trunk/debian/upstream/metadata
trunk/packages/hyphy/trunk/debian/watch
Log:
Add initial packaging for hyphy
Added: trunk/packages/hyphy/trunk/debian/changelog
===================================================================
--- trunk/packages/hyphy/trunk/debian/changelog (rev 0)
+++ trunk/packages/hyphy/trunk/debian/changelog 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,5 @@
+hyphy (2.2.4-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 29 Jun 2015 11:13:57 +0200
Added: trunk/packages/hyphy/trunk/debian/compat
===================================================================
--- trunk/packages/hyphy/trunk/debian/compat (rev 0)
+++ trunk/packages/hyphy/trunk/debian/compat 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1 @@
+9
Added: trunk/packages/hyphy/trunk/debian/control
===================================================================
--- trunk/packages/hyphy/trunk/debian/control (rev 0)
+++ trunk/packages/hyphy/trunk/debian/control 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,29 @@
+Source: hyphy
+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),
+ cmake,
+ mpi-default-dev,
+ libcurl4-gnutls-dev | libcurl4-dev,
+ python,
+ libgtk2.0-dev
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/hyphy/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/hyphy/trunk/
+Homepage: http://hyphy.org/
+
+Package: hyphy
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Hypothesis testing using Phylogenies
+ HyPhy is an open-source software package for the analysis of genetic
+ sequences using techniques in phylogenetics, molecular evolution, and
+ machine learning. It features a complete graphical user interface (GUI)
+ and a rich scripting language for limitless customization of analyses.
+ Additionally, HyPhy features support for parallel computing environments
+ (via message passing interface) and it can be compiled as a shared
+ library and called from other programming environments such as Python or
+ R. Continued development of HyPhy is currently supported in part by an
+ NIGMS R01 award 1R01GM093939.
Added: trunk/packages/hyphy/trunk/debian/copyright
===================================================================
--- trunk/packages/hyphy/trunk/debian/copyright (rev 0)
+++ trunk/packages/hyphy/trunk/debian/copyright 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Spencer V. Muse <muse at stat.ncsu.edu>
+Upstream-Name: HyPhy
+Source: https://github.com/veg/hyphy/releases
+
+Files: *
+Copyright: 1997-2015 Sergei L Kosakovsky Pond <spond at ucsd.edu>
+ Simon D. W. Frost,
+ Spencer V. Muse <muse at stat.ncsu.edu>
+ and others
+License: MIT
+
+Files: debian/*
+Copyright: © 2015 Andreas Tille <tille at debian.org>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER 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.
+
Added: trunk/packages/hyphy/trunk/debian/rules
===================================================================
--- trunk/packages/hyphy/trunk/debian/rules (rev 0)
+++ trunk/packages/hyphy/trunk/debian/rules 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,26 @@
+#!/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 $@ --buildsystem=cmake
+
+override_dh_auto_configure:
+ dh_auto_configure -- -DCMAKE_INSTALL_PREFIX=/usr
+
+override_dh_auto_build:
+ dh_auto_build -- HYPHYGTK
Property changes on: trunk/packages/hyphy/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/hyphy/trunk/debian/source/format
===================================================================
--- trunk/packages/hyphy/trunk/debian/source/format (rev 0)
+++ trunk/packages/hyphy/trunk/debian/source/format 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/hyphy/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/hyphy/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/hyphy/trunk/debian/upstream/metadata 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Sergei L. Kosakovsky Pond and Simon D. W. Frost and Spencer V. Muse
+ Title: "HyPhy: hypothesis testing using phylogenies"
+ Journal: Bioinformatics
+ Year: 2005
+ Volume: 21
+ Number: 5
+ Pages: 676-679
+ DOI: 10.1093/bioinformatics/bti079
+ PMID: 15509596
+ URL: http://bioinformatics.oxfordjournals.org/content/21/5/676.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/21/5/676.full.pdf+html
Added: trunk/packages/hyphy/trunk/debian/watch
===================================================================
--- trunk/packages/hyphy/trunk/debian/watch (rev 0)
+++ trunk/packages/hyphy/trunk/debian/watch 2015-06-29 12:11:38 UTC (rev 19437)
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/veg/hyphy/releases .*/archive/(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
More information about the debian-med-commit
mailing list