debian/0000755000000000000000000000000011667377366007214 5ustar debian/examples0000644000000000000000000000003011667373314010733 0ustar testdata/* debian/tests debian/source/0000755000000000000000000000000011667343512010476 5ustar debian/source/format0000644000000000000000000000001411660156110011671 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000003311667373314010050 0ustar docs/fastDNAml_scripts.txt debian/copyright0000644000000000000000000000370711667373314011143 0ustar This package was debianized by Andreas Tille 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" , Hideo Matsuda , Ray Hagstrom , Ross Overbeek 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. debian/fastDNAml-util0000644000000000000000000000064411667373314011714 0ustar #!/bin/sh BINDIR=/usr/lib/fastdnaml/bin if [ $# -lt 1 ] ; then echo "Usage: $0 " 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 debian/compat0000644000000000000000000000000211667373754010407 0ustar 8 debian/install0000644000000000000000000000007411667377314010577 0ustar debian/fastDNAml-util usr/bin source/fastDNAml usr/bin debian/control0000644000000000000000000000240611667374007010606 0ustar Source: fastdnaml Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Charles Plessy Build-Depends: debhelper (>= 8) Standards-Version: 3.9.2 Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fastdnaml/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fastdnaml/trunk/ Package: fastdnaml Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: phylip Description: 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. . Note that the homepage of this program is not available any more and so this program will probably not see any further updates.debian/links0000644000000000000000000000023211667373314010241 0ustar 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 debian/fastDNAml.10000644000000000000000000000253211667373314011076 0ustar .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/examples/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 , for the Debian GNU/Linux system (but may be used by others). debian/patches/0000755000000000000000000000000011667376413010633 5ustar debian/patches/series0000644000000000000000000000003511667373314012043 0ustar Makefile.patch scripts.patch debian/patches/scripts.patch0000644000000000000000000000327011667373314013342 0ustar Author: unknown Forwarded: No fastDNAml is not maintained upstream anymore. Description: corrects extra spaces, a typo causing a syntax error, and adds a path to the Debian-specific location of some files. License: see debian/copyright --- 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/;/)./' $* debian/patches/Makefile.patch0000644000000000000000000000110011667376413013361 0ustar Author: Andreas Tille Forwarded: No fastDNAml is not maintained upstream anymore. Description: we just need a makefile to let cdbs work properly License: see debian/copyright --- /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 debian/fastDNAml-util ${DESTDIR}/usr/bin + install -m0755 scripts/* ${DESTDIR}/usr/lib/fastdnaml/bin + +clean: + -(cd source; rm -f *.o fastDNAml) + -rm -rf tests + -rm -f checkpoint.* debian/README.Debian0000644000000000000000000000115311667374602011243 0ustar fastdnaml for DEBIAN ---------------------- 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 Mon, 29 Oct 2001 22:34:09 +0100 debian/tests/0000755000000000000000000000000011667373314010343 5ustar debian/tests/Makefile0000644000000000000000000000117311667373314012005 0ustar # Samples and tests by Catherine Letondal 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.* debian/tests/fastdnaml.data0000644000000000000000000000233611667373314013153 0ustar 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 debian/manpages0000644000000000000000000000002311667373314010712 0ustar debian/fastDNAml.1 debian/doc-base.scripts0000644000000000000000000000101611667373314012265 0ustar 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: Science/Biology Format: text Files: /usr/share/doc/fastdnaml/fastDNAml_scripts.txt.gz debian/dirs0000644000000000000000000000005211667377340010065 0ustar usr/share/fastdnaml usr/lib/fastdnaml/bin debian/menu0000644000000000000000000000027711667374613010101 0ustar ?package(fastdnaml):needs="text" section="Applications/Science/Biology"\ title="fastDNAml" command="/usr/bin/fastDNAml-util" \ hints="Construction of phylogenetic trees of DNA sequences" debian/changelog0000644000000000000000000001211511667374530011054 0ustar fastdnaml (1.2.2-10) unstable; urgency=low * debian/control: - Use ftp download site as homepage - Fixed Vcs fields - Standards-Version: 3.9.2 (no changes needed) - Do not Build-Depend cdbs, quilt any more * Debhelper 8 (control + compat) * debian/source/format: 3.0 (quilt) * removed debian/README.source which becomes superfluous by using source format 3.0 (quilt) * Use Debian menu instead of desktop files to not confuse Gnome users Closes: #639996 -- Andreas Tille Tue, 06 Dec 2011 12:08:00 +0100 fastdnaml (1.2.2-9) unstable; urgency=low * Debhelper 7 * Standards-Version 3.8.3 (added README.source) * Added notice about missing upstream homepage in long description * debian/patches/Makefile.patch: Inject this file as patch rather than injecting it into the source directory * debian/fastDNAml-util: Moved this file to the debian directory rather than injecting it into the source directory * debian/rules: removed dh_desktop call -- Andreas Tille Fri, 04 Sep 2009 13:14:01 +0200 fastdnaml (1.2.2-8) unstable; urgency=low * Changed the doc-base section according to the new policy. * debian/control: - Added myself to the uploaders field. - Removed the [Biology] tag from the short description. * debian/patches/{fast*,Makefile.diff,tests.patch} shipped some plain files as patches. I created the files properly and deleted the corresopnding patches. * Annotated debian/patches/scripts.patch according to Debian-Med's policy. * Corrected a link in debian/fastDNAml.1. -- Charles Plessy Sun, 06 Jul 2008 18:42:52 +0900 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 - DM-Upload-Allowed: yes - Uploaders: Andreas Tille - Vcs-Browser, Vcs-Svn * Removed encoding tag from desktop file -- Andreas Tille 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 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 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 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 Tue, 30 Oct 2001 12:02:41 +0100 fastdnaml (1.2.2-2) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk 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 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 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 Thu, 20 May 1999 15:49:23 +0200 fastdnaml (1.0.8-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Thu, 3 Dec 1998 16:55:30 +0100 debian/doc-base.fastdnaml0000644000000000000000000000053611667373314012555 0ustar 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: Science/Biology Format: text Files: /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt debian/rules0000755000000000000000000000131011667377366010267 0ustar #!/usr/bin/make -f # debian/rules for fastDNAml using dh # Andreas Tille , GPL %: dh $@ # dh_clean expects a Makefile which was just removed by redoing the patches ... # This hack circumvents the problem override_dh_clean: rm -fr source/fastDNAml override_dh_auto_install: # do nothing override_dh_install: dh_install 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/*