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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
