[med-svn] r6147 - in trunk/packages: . fasttree fasttree/trunk fasttree/trunk/debian fasttree/trunk/debian/patches fasttree/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Wed Mar 2 18:11:44 UTC 2011
Author: moeller
Date: 2011-03-02 18:11:40 +0000 (Wed, 02 Mar 2011)
New Revision: 6147
Added:
trunk/packages/fasttree/
trunk/packages/fasttree/trunk/
trunk/packages/fasttree/trunk/debian/
trunk/packages/fasttree/trunk/debian/README.Debian
trunk/packages/fasttree/trunk/debian/changelog
trunk/packages/fasttree/trunk/debian/compat
trunk/packages/fasttree/trunk/debian/control
trunk/packages/fasttree/trunk/debian/copyright
trunk/packages/fasttree/trunk/debian/docs
trunk/packages/fasttree/trunk/debian/fasttree.dirs
trunk/packages/fasttree/trunk/debian/fasttree.install
trunk/packages/fasttree/trunk/debian/patches/
trunk/packages/fasttree/trunk/debian/patches/Makefile.patch
trunk/packages/fasttree/trunk/debian/patches/series
trunk/packages/fasttree/trunk/debian/rules
trunk/packages/fasttree/trunk/debian/source/
trunk/packages/fasttree/trunk/debian/source/format
Log:
First shot at fasttree (to help qiime)
Property changes on: trunk/packages/fasttree/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/fasttree/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fasttree/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/fasttree/trunk/debian/README.Debian 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,8 @@
+fasttree for Debian
+-------------------
+
+Please help with
+
+ * man pages
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 18:52:56 +0100
Added: trunk/packages/fasttree/trunk/debian/changelog
===================================================================
--- trunk/packages/fasttree/trunk/debian/changelog (rev 0)
+++ trunk/packages/fasttree/trunk/debian/changelog 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,5 @@
+fasttree (2.1.0.c-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Mar 2011 18:52:56 +0100
Added: trunk/packages/fasttree/trunk/debian/compat
===================================================================
--- trunk/packages/fasttree/trunk/debian/compat (rev 0)
+++ trunk/packages/fasttree/trunk/debian/compat 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1 @@
+7
Added: trunk/packages/fasttree/trunk/debian/control
===================================================================
--- trunk/packages/fasttree/trunk/debian/control (rev 0)
+++ trunk/packages/fasttree/trunk/debian/control 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,30 @@
+Source: fasttree
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.1
+Homepage: http://www.microbesonline.org/fasttree/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/fasttree/trunk/
+
+Package: fasttree
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: <insert up to 60 chars description>
+ FastTree infers approximately-maximum-likelihood phylogenetic trees from
+ alignments of nucleotide or protein sequences. It handles alignments
+ with up to a million of sequences in a reasonable amount of time and
+ memory. For large alignments, FastTree is 100-1,000 times faster than
+ PhyML 3.0 or RAxML 7.
+ .
+ FastTree is more accurate than PhyML 3 with default settings, and much
+ more accurate than the distance-matrix methods that are traditionally
+ used for large alignments. FastTree uses the Jukes-Cantor or generalized
+ time-reversible (GTR) models of nucleotide evolution and the JTT
+ (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
+ for the varying rates of evolution across sites, FastTree uses a single
+ rate for each site (the "CAT" approximation). To quickly estimate the
+ reliability of each split in the tree, FastTree computes local support
+ values with the Shimodaira-Hasegawa test (these are the same as PhyML
+ 3's "SH-like local supports").
Added: trunk/packages/fasttree/trunk/debian/copyright
===================================================================
--- trunk/packages/fasttree/trunk/debian/copyright (rev 0)
+++ trunk/packages/fasttree/trunk/debian/copyright 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,41 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: fasttree
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+Copyright: (C) 2008-2009 The Regents of the University of California
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+# Please choose a license for your packaging work. If the program you package
+# uses a mainstream license, using the same license is the safest choice.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
+# If you just want it to be GPL version 3, leave the following line in.
+
+and is licensed under the GPL version 3, see above.
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/fasttree/trunk/debian/fasttree.dirs
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttree.dirs (rev 0)
+++ trunk/packages/fasttree/trunk/debian/fasttree.dirs 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/fasttree/trunk/debian/fasttree.install
===================================================================
--- trunk/packages/fasttree/trunk/debian/fasttree.install (rev 0)
+++ trunk/packages/fasttree/trunk/debian/fasttree.install 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1 @@
+fasttree usr/bin
Added: trunk/packages/fasttree/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/fasttree/trunk/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/fasttree/trunk/debian/patches/Makefile.patch 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,11 @@
+Index: fasttree-2.1.0.c/Makefile
+===================================================================
+--- /dev/null 1970-01-01 00:00:00.000000000 +0000
++++ fasttree-2.1.0.c/Makefile 2011-03-02 19:07:11.000000000 +0100
+@@ -0,0 +1,6 @@
++
++fasttree: fasttree.c
++ $(CC) $(CFLAGS) -o $@ $< -lm
++
++distclean clean:
++ rm -f fasttree
Added: trunk/packages/fasttree/trunk/debian/patches/series
===================================================================
--- trunk/packages/fasttree/trunk/debian/patches/series (rev 0)
+++ trunk/packages/fasttree/trunk/debian/patches/series 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1 @@
+Makefile.patch
Added: trunk/packages/fasttree/trunk/debian/rules
===================================================================
--- trunk/packages/fasttree/trunk/debian/rules (rev 0)
+++ trunk/packages/fasttree/trunk/debian/rules 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
Property changes on: trunk/packages/fasttree/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/fasttree/trunk/debian/source/format
===================================================================
--- trunk/packages/fasttree/trunk/debian/source/format (rev 0)
+++ trunk/packages/fasttree/trunk/debian/source/format 2011-03-02 18:11:40 UTC (rev 6147)
@@ -0,0 +1 @@
+3.0 (quilt)
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