[med-svn] r1433 - in trunk/packages: . fastdnaml fastdnaml/tags fastdnaml/trunk fastdnaml/trunk/debian fastdnaml/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Feb 18 15:07:04 UTC 2008
Author: tille
Date: 2008-02-18 15:07:02 +0000 (Mon, 18 Feb 2008)
New Revision: 1433
Added:
trunk/packages/fastdnaml/
trunk/packages/fastdnaml/tags/
trunk/packages/fastdnaml/tags/1.2.2-7/
trunk/packages/fastdnaml/trunk/
trunk/packages/fastdnaml/trunk/debian/
trunk/packages/fastdnaml/trunk/debian/README.Debian
trunk/packages/fastdnaml/trunk/debian/changelog
trunk/packages/fastdnaml/trunk/debian/compat
trunk/packages/fastdnaml/trunk/debian/control
trunk/packages/fastdnaml/trunk/debian/copyright
trunk/packages/fastdnaml/trunk/debian/dirs
trunk/packages/fastdnaml/trunk/debian/doc-base.fastdnaml
trunk/packages/fastdnaml/trunk/debian/doc-base.scripts
trunk/packages/fastdnaml/trunk/debian/docs
trunk/packages/fastdnaml/trunk/debian/examples
trunk/packages/fastdnaml/trunk/debian/fastdnaml.desktop
trunk/packages/fastdnaml/trunk/debian/install
trunk/packages/fastdnaml/trunk/debian/links
trunk/packages/fastdnaml/trunk/debian/manpages
trunk/packages/fastdnaml/trunk/debian/patches/
trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff
trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff
trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch
trunk/packages/fastdnaml/trunk/debian/patches/series
trunk/packages/fastdnaml/trunk/debian/patches/tests.patch
trunk/packages/fastdnaml/trunk/debian/rules
Log:
Added fastdnaml.
Added: trunk/packages/fastdnaml/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/README.Debian 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,23 @@
+fastdnaml for DEBIAN
+----------------------
+
+I decided to continue packaging the program which was orphaned because
+I needed it for packaging Arb.
+
+Since fastDNAml comes with several different utilities,
+which having names which may conflict with other Unix programs
+the Debian installation uses a wrapper, named "fastDNAml-util",
+which is used to invoke the specific programs.
+
+So, to run frequencies, you type:
+
+fastDNAml-util frequencies
+
+If it bothers you, just add "/usr/lib/fastdnaml/bin" in front of
+your PATH and you'll get the fastDNAml programs as usual.
+
+Test files and samples are in /usr/share/doc/fastdnaml/examples/tests.
+Just type make.
+
+
+Andreas Tille <tille at debian.org> Mon, 29 Oct 2001 22:34:09 +0100
Added: trunk/packages/fastdnaml/trunk/debian/changelog
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/changelog (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/changelog 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,101 @@
+fastdnaml (1.2.2-7) unstable; urgency=low
+
+ * Homepage of project vanished, used archive.org as homepage tag
+ * Removed XB-Tag which is not used
+ * debian/rules: Do not auto generate debian/control, removed
+ debian/control.in
+ * Standards-Version: 3.7.3 (no changes needed)
+ * Switched to quilt
+ * Group maintenance
+ - Maintainer: Debian-Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+ - DM-Upload-Allowed: yes
+ - Uploaders: Andreas Tille <tille at debian.org>
+ - Vcs-Browser, Vcs-Svn
+ * Removed encoding tag from desktop file
+
+ -- Andreas Tille <tille at debian.org> Mon, 18 Feb 2008 14:20:49 +0100
+
+fastdnaml (1.2.2-6) unstable; urgency=low
+
+ * Switched to cdbs
+ * Standards-Version: 3.7.2 (no changes necessary)
+ * Setting DebTags
+ * Added desktop file
+
+ -- Andreas Tille <tille at debian.org> Sat, 9 Sep 2006 10:56:41 +0200
+
+fastdnaml (1.2.2-5) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Use debian/compat for debhelper compatibility
+ * Changed compile option from -g to -Wall
+ * Added documentation to doc-base
+ * Fixed typo in scripts/iterate_rates
+
+ -- Andreas Tille <tille at debian.org> Sat, 26 Apr 2003 14:46:00 +0200
+
+fastdnaml (1.2.2-4) unstable; urgency=low
+
+ * Install fastDNAml_doc_1.2.txt as NCBI Vibrant Toolkit compatible
+ helpfile instead of just putting it just into /usr/share/doc/fastdnaml.
+
+ -- Andreas Tille <tille at debian.org> Sat, 3 Nov 2001 20:55:22 +0100
+
+fastdnaml (1.2.2-3) unstable; urgency=low
+
+ * New maintainer
+ closes: #100220
+ * Standards-Version: 3.5.6
+ * Added URL to the package description because I consider this as
+ "good style" to have an upstream link without installing the package
+ * Included the text of the upstrem source file "license" into copyright
+
+ -- Andreas Tille <tille at debian.org> Tue, 30 Oct 2001 12:02:41 +0100
+
+fastdnaml (1.2.2-2) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 23:00:44 +0200
+
+fastdnaml (1.2.2-1) unstable; urgency=low
+
+ * New upstream release; closes: #60862
+ * Corrected name of README.debian to README.Debian.
+ * Updated package to latest standards version.
+ * Updated download URL in copyright file.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sun, 20 May 2001 17:53:37 +0200
+
+fastdnaml (1.2.1-2) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: #92795
+ * Updated to latest standards version and added Build-Depends (changed
+ control, copyright, dirs, and rules);
+ closes: #91153, #91440
+ * Removed empty docs file.
+ * Added homepage to copyright file.
+ * Corrected doc path in manpage.
+ * Moved package from misc to section science, because it is a tool that
+ is exclusively useful for molecular biologists.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sat, 21 Apr 2001 09:16:26 +0200
+
+fastdnaml (1.2.1-1) unstable; urgency=low
+
+ * A manual page. Closes #32786
+ * The wrapper now displays the name of available programs. Closes #33383
+ * New upstream release. Closes #32787. Warning: the usage changed drastically
+ (the Makefile in the tests directory reflect that).
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Thu, 20 May 1999 15:49:23 +0200
+
+fastdnaml (1.0.8-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Thu, 3 Dec 1998 16:55:30 +0100
Added: trunk/packages/fastdnaml/trunk/debian/compat
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/compat (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/compat 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1 @@
+5
Added: trunk/packages/fastdnaml/trunk/debian/control
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/control (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/control 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,25 @@
+Source: fastdnaml
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), quilt, debhelper (>= 5)
+Standards-Version: 3.7.3
+Homepage: http://web.archive.org/web/20061017161001/http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fastdnaml/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/fastdnaml/trunk/
+
+Package: fastdnaml
+Architecture: any
+Depends: ${shlibs:Depends}
+Suggests: phylip
+Description: [Biology] Tool for construction of phylogenetic trees of DNA sequences
+ fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+ (part of his PHYLIP package). Users should consult the documentation for
+ DNAML before using this program.
+ .
+ fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+ faster and using less memory, so that larger trees and/or more bootstrap
+ replicates become tractable. Much of fastDNAml is merely a recoding of the
+ PHYLIP 3.3 DNAML program from PASCAL to C.
Added: trunk/packages/fastdnaml/trunk/debian/copyright
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/copyright (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/copyright 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,50 @@
+This package was debianized by Andreas Tille <tille at debian.org> on
+Mon, 29 Oct 2001 22:34:09 +0100.
+
+It was downloaded from http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
+Homepage: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
+ Note: This Homepage vanished and seems to have no replacement
+
+Upstream Authors: "Gary J. Olsen" <gary at phylo.life.uiuc.edu>,
+ Hideo Matsuda <matsuda at mcs.anl.gov>,
+ Ray Hagstrom <hagstrom at mcs.anl.gov>,
+ Ross Overbeek <overbeek at mcs.anl.gov>
+
+
+Copyright (C) 1998, 1999, 2000 by Gary J. Olsen
+
+License: GPL (since January 1999)
+
+
+This program is free software; you may redistribute it and/or modify it
+under the terms of the GNU General Public License as published by the Free
+Software Foundation; either version 2 of the License, or (at your option)
+any later version.
+
+This program 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.
+
+On Debian systems, the complete text of the GNU General Public
+Licence can be found in /usr/share/common-licenses/GPL file.
+
+fastDNAml is based in part on the program dnaml by Joseph Felsenstein.
+
+Copyright notice from dnaml:
+
+ version 3.3. (c) Copyright 1986, 1990 by the University of Washington
+ and Joseph Felsenstein. Written by Joseph Felsenstein. Permission is
+ granted to copy and use this program provided no fee is charged for it
+ and provided that this copyright notice is not removed.
+
+When publishing work that based on results from fastDNAml please cite:
+
+ Felsenstein, J. 1981. Evolutionary trees from DNA sequences:
+ A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
+
+and
+
+ Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994.
+ fastDNAml: A tool for construction of phylogenetic trees of DNA
+ sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.
Added: trunk/packages/fastdnaml/trunk/debian/dirs
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/dirs (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/dirs 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,2 @@
+usr/share/fastdnaml
+usr/lib/fastdnaml/bin
Added: trunk/packages/fastdnaml/trunk/debian/doc-base.fastdnaml
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/doc-base.fastdnaml (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/doc-base.fastdnaml 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,10 @@
+Document: fastdnaml
+Title: FastDNAml 1.2
+Author: Gary J. Olsen
+Abstract: FastDNAml is a program derived from Joseph Felsenstein's version
+ 3.3 DNAML (part of his PHYLIP package). Users should consult the
+ documentation for DNAML before using this program.
+Section: Apps/Science
+
+Format: text
+Files: /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt
Added: trunk/packages/fastdnaml/trunk/debian/doc-base.scripts
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/doc-base.scripts (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/doc-base.scripts 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,12 @@
+Document: fastdnaml-scripts
+Title: Shell Scripts for use with fastDNAml and DNArates
+Author: Gary J. Olsen
+Abstract: UNIX shell scripts have proven quite useful in running the fastDNAml
+ and/or DNArates programs. They have been used in two different contexts.
+ First, many of the program options can be invoked by simple editing of the
+ input. The second category are scripts that help run and maintain results of
+ the program.
+Section: Apps/Science
+
+Format: text
+Files: /usr/share/doc/fastdnaml/fastDNAml_scripts.txt.gz
Added: trunk/packages/fastdnaml/trunk/debian/docs
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/docs (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/docs 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1 @@
+docs/fastDNAml_scripts.txt
Added: trunk/packages/fastdnaml/trunk/debian/examples
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/examples (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/examples 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,2 @@
+testdata/*
+tests
Added: trunk/packages/fastdnaml/trunk/debian/fastdnaml.desktop
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/fastdnaml.desktop (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/fastdnaml.desktop 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,11 @@
+[Desktop Entry]
+Version=1.0
+Terminal=false
+Exec=fastDNAml
+Name=fastDNAml
+GenericName=Phylogenetic tree construction
+GenericName[en]=Phylogenetic tree construction
+Comment=Tool for construction of phylogenetic trees of DNA sequences
+Comment[en]=Tool for construction of phylogenetic trees of DNA sequences
+Type=Application
+Categories=Biology;Science;Education;
Added: trunk/packages/fastdnaml/trunk/debian/install
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/install (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/install 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,3 @@
+fastDNAml-util usr/bin
+source/fastDNAml usr/bin
+debian/*.desktop usr/share/applications
Added: trunk/packages/fastdnaml/trunk/debian/links
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/links (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/links 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,2 @@
+usr/share/fastdnaml/fastdnaml_help usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt
+usr/share/man/man1/fastDNAml.1 usr/share/man/man1/fastDNAml-util.1
Added: trunk/packages/fastdnaml/trunk/debian/manpages
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/manpages (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/manpages 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1 @@
+fastDNAml.1
Added: trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/Makefile.diff 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,16 @@
+--- /dev/null
++++ fastdnaml-1.2.2/Makefile
+@@ -0,0 +1,13 @@
++all: fastDNAml
++
++fastDNAml:
++ (cd source; cc ${CFLAGS} fastDNAml.c -o fastDNAml -lm)
++
++install:
++ install -m0755 source/fastDNAml fastDNAml-util ${DESTDIR}/usr/bin
++ install -m0755 scripts/* ${DESTDIR}/usr/lib/fastdnaml/bin
++
++clean:
++ -(cd source; rm -f *.o fastDNAml)
++ -(cd tests.fastDNAml; $(MAKE) clean)
++ -rm -f checkpoint.*
Added: trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml-util.diff 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,27 @@
+--- /dev/null
++++ fastdnaml-1.2.2/fastDNAml-util
+@@ -0,0 +1,24 @@
++#!/bin/sh
++
++BINDIR=/usr/lib/fastdnaml/bin
++
++if [ $# -lt 1 ] ; then
++ echo "Usage: $0 <utility>" 1>&2
++ echo " Existing utilities are:"
++ ls ${BINDIR}
++ exit 1
++fi
++
++WRAPPER=$0
++PROGRAM=$1
++shift
++ARGS=$*
++
++if [ -x ${BINDIR}/${PROGRAM} ]; then
++ exec ${BINDIR}/${PROGRAM} ${ARGS}
++else
++ echo "Usage: utility ${PROGRAM} does not exist in fastDNAml"
++ echo " Existing utilities are:"
++ ls ${BINDIR}
++ exit 1
++fi
Added: trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastDNAml.1.diff 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,44 @@
+--- /dev/null
++++ fastdnaml-1.2.2/fastDNAml.1
+@@ -0,0 +1,41 @@
++.TH fastDNAml 1
++.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
++.\" other parms are allowed: see man(7), man(1)
++.SH NAME
++fastDNAml \- DNA Maximum Likelihood program
++.SH SYNOPSIS
++.B fastDNAml
++.I "< infile > outfile"
++.PP
++.B fastDNAml-util
++.I " utility"
++.SH "DESCRIPTION"
++.B fastDNAml
++is derived from Joseph Felsenstein's version 3.3 DNAML.
++.PP
++This manual page documents briefly the
++.B fastDNAml
++and
++.B fastDNAml-util
++commands.
++This manual page was written for the Debian GNU/Linux distribution
++because the original program does not have a manual page.
++Instead, it has documentation in text format. See below.
++.SH OPTIONS
++No options on the command line. They are supplied in the input file.
++Some of the utilities scripts may help you to add options. Type
++.B fastDNAml-util
++alone to get the list of utilities.
++For instance,
++.B fastDNAml-util global
++will add the 'G' (for global) option to its standard input and will send
++it to standard output. See examples in
++.IR /usr/share/doc/fastdnaml/tests/Makefile.
++.SH "SEE ALSO"
++The programs are documented fully in
++.IR /usr/share/doc/fastdnaml.
++Since fastDNAml is based on Phylip's DNAML, reading the documentation of
++Phylip is recommended, too.
++.SH AUTHOR
++This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
++for the Debian GNU/Linux system (but may be used by others).
Added: trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/fastdnaml-1.2.1.announce.diff 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,7 @@
+--- /dev/null
++++ fastdnaml-1.2.2/fastdnaml-1.2.1.announce
+@@ -0,0 +1,4 @@
++Warning: fastDNAml 1.2 changed drastically its user interface. Many utilities
++like "frequencies" are no longer necessary. Many default options changed.
++See the documentation or the Makefile in the tests directory.
++
Added: trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/scripts.patch 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,60 @@
+--- fastdnaml-1.2.2.orig/scripts/fastDNAml_boot
++++ fastdnaml-1.2.2/scripts/fastDNAml_boot
+@@ -1,5 +1,8 @@
+-#! /bin/sh
++#!/bin/sh
+ #
++
++PATH=/usr/lib/fastdnaml/bin:${PATH}
++
+ comm=`echo "$0" | sed -e 's&^.*/&&g'`
+ bootflag="-boots"
+ cleanflag="-noclean"
+--- fastdnaml-1.2.2.orig/scripts/fastDNAml_loop
++++ fastdnaml-1.2.2/scripts/fastDNAml_loop
+@@ -1,5 +1,8 @@
+-#! /bin/sh
++#!/bin/sh
+ #
++
++PATH=/usr/lib/fastdnaml/bin:${PATH}
++
+ comm=`echo "$0" | sed -e 's&^.*/&&'`
+ cleanflag="-noclean"
+ maxflag="-max"
+--- fastdnaml-1.2.2.orig/scripts/iterate_rates
++++ fastdnaml-1.2.2/scripts/iterate_rates
+@@ -1,7 +1,9 @@
+-#! /bin/sh
++#!/bin/sh
+ #
+ # iterate_rates file_name_root program_options [cycles]
+
++PATH=/usr/lib/fastdnaml/bin:${PATH}
++
+ if test $# -lt 2; then
+ echo "Usage: iterate_rates file_name_root [cycles]";
+ exit
+@@ -9,7 +11,7 @@
+
+ root0="$1"
+ if test -f "${root0}.phylip"; then suf=phylip
+-elit test -f "${root0}.phy"; then suf=phy
++elif test -f "${root0}.phy"; then suf=phy
+ else
+ echo "Could not find sequence file ${root0}.phy[lip]"
+ exit
+--- fastdnaml-1.2.2.orig/scripts/scores
++++ fastdnaml-1.2.2/scripts/scores
+@@ -1,3 +1,3 @@
+-#! /bin/sh
++#!/bin/sh
+ #
+ grep '^Ln Likelihood' $* /dev/null | sed 's/^\([^:]*\):\(.*\)$/\2 (file: \1)/g' | sort -nr +3
+--- fastdnaml-1.2.2.orig/scripts/trees2prolog
++++ fastdnaml-1.2.2/scripts/trees2prolog
+@@ -1,3 +1,3 @@
+-#! /bin/sh
++#!/bin/sh
+ #
+ sed -e 's/^/pseudoNewick(/' -e 's/] /], /' -e 's/;/)./' $*
Added: trunk/packages/fastdnaml/trunk/debian/patches/series
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/series (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/series 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,6 @@
+fastdnaml-1.2.1.announce.diff
+fastDNAml.1.diff
+fastDNAml-util.diff
+Makefile.diff
+scripts.patch
+tests.patch
Added: trunk/packages/fastdnaml/trunk/debian/patches/tests.patch
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/patches/tests.patch (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/patches/tests.patch 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,48 @@
+--- /dev/null
++++ fastDNAml_1.2.2/tests/Makefile
+@@ -0,0 +1,22 @@
++# Samples and tests by Catherine Letondal <letondal at pasteur.fr>
++
++
++test: fastDNAml fastDNAml_boot
++
++oldfastDNAml:
++ cat fastdnaml.data | fastDNAml-util frequencies | fastDNAml-util printdata | fastDNAml-util treefile | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
++
++fastDNAml:
++ cat fastdnaml.data | fastDNAml-util printdata | fastDNAml > fastdnaml.out ; fastDNAml-util clean_checkpoints
++
++fastDNAml_boot:
++ cat fastdnaml.data | fastDNAml-util printdata > fastdnaml.data.tmp; fastDNAml-util fastDNAml_boot -out -boots 2 -max 2 fastdnaml.data.tmp 2
++
++clean:
++ rm -f *.tmp*
++ rm -f *.out
++ rm -f treefile*
++ rm -f checkpoint.*
++
++
++
+--- /dev/null
++++ fastDNAml_1.2.2/tests/fastdnaml.data
+@@ -0,0 +1,20 @@
++ 4 232
++Bovine CCAAAAACCC CTTGTCCCCC CTCCCCTTTA AAACCCCCAA AAAACCCTTA AACCCCAAAA
++Mouse CCAAAAAAAA AAAACTCCAA AACCCCCCCA CCCCCCCCTA AGGTCCCCCA AACCCAGGGG
++Gorilla CCCCAAATTT TTTATCATAA AACCCCCCCA AAACCCCCCA ACCCAAACCA AACCCTTTTT
++Human CCCCAAACCC TCCACCATCC AACCCCCCCA AAACTTTTCA ACCTAAACCA AATTTTTTTT
++
++ AATAACACCC ACTACCCAAA AAAATATTCC CAAACACTCC AAAAAATACC CCCCCAACCC
++ AATAATACCC CCAACCCAAA AAAACAAACC TAAATACCTC AAAAAACACC CCCCCAATCC
++ GACCCCCCCC CTCGCCCGGA AAAACAAATT CAAACACCTC AAAAAACACC CCTTCAGCTC
++ AACCCTCCCC CCAACCCGGA AAGGCAAATT CAAACACCTC AAAGGGCACC CCTCCAACCC
++
++ GCCCACCCCC CAACCCCCCC CCCCTTGCCC CACGGTCACC CAACCCCTTT CTTTCACCCA
++ ACCCGCCCCC CAACCCCTTT TTCCCCGCCC CATGGCCACC AAATCCTCCC CCCCTACCCA
++ ATTTACCCCC TAACCCTTTT CCCCTTACCC CACGGTCACC AAATCCCCCC CTTTCACCCA
++ GCCCACCCTT CAACCCCCCC CCTTCCGTTT TACGGCTACC AAATCCCCCC CTTTCACCCA
++
++ ACCCCAACCA ACCCTCCCAA AAAAACCAAA CCCAAACCCA CCGCCCAACC AA
++ ACCCCAACCA ACCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
++ ATCCCGGTTG GCCCCCCCAA AAAAACCAAA TTTAAACCCA AAACCCCCCC AA
++ ACCCCAATTA ACCCTTTCAA AAAAACCAAA TTTGGGCCCC AAACCCCCCC AA
Added: trunk/packages/fastdnaml/trunk/debian/rules
===================================================================
--- trunk/packages/fastdnaml/trunk/debian/rules (rev 0)
+++ trunk/packages/fastdnaml/trunk/debian/rules 2008-02-18 15:07:02 UTC (rev 1433)
@@ -0,0 +1,19 @@
+#!/usr/bin/make -f
+# debian/rules for fastDNAml using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+# dh_clean expects a Makefile which was just removed by redoing the patches ...
+# This hack circumvents the problem
+clean::
+ rm -fr source/fastDNAml
+
+install/fastdnaml::
+ cp -a docs/fastDNAml_doc_1.2.txt `pwd`/debian/`dh_listpackages`/usr/share/`dh_listpackages`/fastdnaml_help
+ # the scripts have to be executable thus mentioning these in debian/install is not enough
+ cp -a scripts/* `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin
+ chmod 755 `pwd`/debian/`dh_listpackages`/usr/lib/`dh_listpackages`/bin/*
+ dh_desktop
Property changes on: trunk/packages/fastdnaml/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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