Author: plessy Date: 2009-07-07 10:41:08 +0000 (Tue, 07 Jul 2009) New Revision: 3589
Removed: trunk/packages/seaview/trunk/debian/seaview.1 trunk/packages/seaview/trunk/debian/seaview.1.xml Modified: trunk/packages/seaview/trunk/debian/changelog trunk/packages/seaview/trunk/debian/control trunk/packages/seaview/trunk/debian/copyright trunk/packages/seaview/trunk/debian/manpages Log: New upstream version adding nucleotide ambiguity symbols in consensus DNA sequences and adopting the manpages made in Debian. Modified: trunk/packages/seaview/trunk/debian/changelog =================================================================== --- trunk/packages/seaview/trunk/debian/changelog 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/changelog 2009-07-07 10:41:08 UTC (rev 3589) @@ -1,3 +1,15 @@ +seaview (1:4.1-1) UNRELEASED; urgency=low + + TODO: Get permission to use autobuilders. + + * New upstream version adding nucleotide ambiguity symbols in consensus + DNA sequences. + * debian/control: checked package conformance with Policy 3.8.2 + and incremented Standards-Version accordingly (no changes needed). + * debian/seaview.1*: accepted upstream and therefore deleted. + + -- Charles Plessy <[email protected]> Tue, 07 Jul 2009 19:14:43 +0900 + seaview (1:4.0-1) unstable; urgency=low * New upstream version Modified: trunk/packages/seaview/trunk/debian/control =================================================================== --- trunk/packages/seaview/trunk/debian/control 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/control 2009-07-07 10:41:08 UTC (rev 3589) @@ -5,7 +5,7 @@ DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> Build-Depends: debhelper ( >= 7 ), libfltk1.1-dev, libjpeg62-dev, libpng12-dev, libxft-dev, libxext-dev, zlib1g-dev -Standards-Version: 3.8.1 +Standards-Version: 3.8.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seaview/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seaview/trunk/ Homepage: http://pbil.univ-lyon1.fr/software/seaview.html Modified: trunk/packages/seaview/trunk/debian/copyright =================================================================== --- trunk/packages/seaview/trunk/debian/copyright 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/copyright 2009-07-07 10:41:08 UTC (rev 3589) @@ -1,110 +1,116 @@ -Format: Machine-readable license summary, see http://dep.debian.net/deps/dep5/ +Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’. -Name: SeaView -Contact: Manolo Gouy <[email protected]> -Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.0.tar.gz -Disclamer: - This package is not part of the Debian operating system. The seaview source - and binary Debian packages are part of the “non-free” area in our archive. The - packages in this area are not part of the Debian system, although they have - been configured for use with Debian. We nevertheless support the use of the - seaview source and binary Debian pacakges and provide infrastructure for - non-free packages (such as our bug tracking system and mailing lists). The - licences of SeaView do not forbid Debian from using autobuilders to create - binary packages. +Name : SeaView +Contact : Manolo Gouy <[email protected]> +Source : ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.1.tar.gz +Disclamer : This package is not part of the Debian operating system. + The seaview source and binary Debian packages are part of the “non-free” area + in our archive. The packages in this area are not part of the Debian system, + although they have been configured for use with Debian. We nevertheless support + the use of the seaview source and binary Debian pacakges and provide + infrastructure for non-free packages (such as our bug tracking system and + mailing lists). The licences of SeaView do not forbid Debian from using + autobuilders to create binary packages. + Copyright: 1996-2009 Manolo Gouy <[email protected]> -License: GPL-2+ with PHYLIP exemption. - This program, except where indicated, 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 2 of the License, or (at your option) any later version. - . - Two files (dnapars.c and protpars.c) have a distinct copyright - which authorizes distribution that does not generate revenue. - . - 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. - . - A copy of the GNU General Public License is available - from http://www.gnu.org/licenses/gpl.txt or by mail from the Free Software - Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - USA. -Comment: On Debian systems, the complete text of the GNU General - Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. -Comment: Manolo Gouy confirmed to Charles Plessy that SeaView provides a - similar exemption regarding the files dnapars.c and protpars.c originating from - the PHYLIP phylogeny package, see below. -Comment: If you use SeaView in a published work, please cite the following reference: - Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic - tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., - 12, 543-548. +License: GPL-3+ with PHYLIP exemption. + + This program, except where indicated, 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.. + + Two files (dnapars.c and protpars.c) have a distinct license + which authorizes distribution that does not generate revenue. + + Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered by the + GNU General Public License but are copyright Stephane Guindon. + + 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. + + Additional permission under GNU GPL version 3 section 7 + + If you modify this Program, or any covered work, by linking or combining it with PHYLIP + (or a modified version of that library), containing parts covered by the terms of + the University of Washington license, the licensor of this Program grants you additional + permission to convey the resulting work. + + A copy of the GNU General Public License is available + from http://www.gnu.org/licenses/gpl.txt . +On Debian systems, the complete text of the GNU General Public License version +3 can be found in ‘/usr/share/common-licenses/GPL-3’. + Files: csrc/bionj.c, csrc/phyml_util.h Copyright: © Stephane Guindon. Oct 2003 onward License: GPL-2+ with PHYLIP exemption. - 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 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. - . - You should have received a copy of the GNU General Public License along with this program; if not, - see <http://www.gnu.org/licenses>. - . - Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. - Thus, the terms and conditions of the GNU General Public License cover the whole combination. - . - In addition, as a special exception, the copyright holders of PHYML give you permission to combine - PHYML with free software programs or libraries that are released under the GNU LGPL and with code - included in the standard release of PHYLIP under the University of Washington license (or modified - versions of such code, with unchanged license). You may copy and distribute such a system following - the terms of the GNU GPL for PHYML and the licenses of the other code concerned. - . - Note that people who make modified versions of PHYML are not obligated to grant this special exception - for their modified versions; it is their choice whether to do so. The GNU General Public License gives - permission to release a modified version without this exception; this exception also makes it possible - to release a modified version which carries forward this exception. + + 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 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. + + You should have received a copy of the GNU General Public License along with this program; if not, + see <http://www.gnu.org/licenses>. + + Linking PHYML statically or dynamically with other modules is making a combined work based on PHYML. + Thus, the terms and conditions of the GNU General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of PHYML give you permission to combine + PHYML with free software programs or libraries that are released under the GNU LGPL and with code + included in the standard release of PHYLIP under the University of Washington license (or modified + versions of such code, with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for PHYML and the licenses of the other code concerned. + + Note that people who make modified versions of PHYML are not obligated to grant this special exception + for their modified versions; it is their choice whether to do so. The GNU General Public License gives + permission to release a modified version without this exception; this exception also makes it possible + to release a modified version which carries forward this exception. Files: csrc/dnapars.c, csrc/protpars.c License: - (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is - granted to reproduce, perform, and modify these programs and documentation files. - Permission is granted to distribute or provide access to these programs provided - that this copyright notice is not removed, the programs are not integrated with or - called by any product or service that generates revenue, and that your distribution - of these documentation files and programs are free. Any modified versions of these - materials that are distributed or accessible shall indicate that they are based on - these programs. Institutions of higher education are granted permission to - distribute this material to their students and staff for a fee to recover - distribution costs. Permission requests for any other distribution of these - program should be directed to license (at) u.washington.edu . + + (c) Copyright 1980-2008. University of Washington. All rights reserved. Permission is + granted to reproduce, perform, and modify these programs and documentation files. + Permission is granted to distribute or provide access to these programs provided + that this copyright notice is not removed, the programs are not integrated with or + called by any product or service that generates revenue, and that your distribution + of these documentation files and programs are free. Any modified versions of these + materials that are distributed or accessible shall indicate that they are based on + these programs. Institutions of higher education are granted permission to + distribute this material to their students and staff for a fee to recover + distribution costs. Permission requests for any other distribution of these + program should be directed to license (at) u.washington.edu . Files: FL/* Copyright: © 2004 Greg Ercolano © 2005 Nathan Vander Wilt License: LGPL-2+ - This library is free software; you can redistribute it and/or - modify it under the terms of the GNU Library General Public - License as published by the Free Software Foundation; either - version 2 of the License, or (at your option) any later version. - . - This library 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 - Library General Public License for more details. - . - You should have received a copy of the GNU Library General Public - License along with this library; if not, write to the Free Software - Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA -Comment: On Debian systems, the complete text of the GNU Lesser General - Public License version 2 can be found in `/usr/share/common-licenses/LGPL-2'. + + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Library General Public + License as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later version. + + This library 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 + Library General Public License for more details. + + You should have received a copy of the GNU Library General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA +On Debian systems, the complete text of the GNU Lesser General Public License +version 2 can be found in ‘/usr/share/common-licenses/LGPL-2’. + Files: debian/* Copyright: © 1999 Stephane Bortzmeyer <[email protected]> © 2001 Dr. Guenter Bechly <[email protected]> Modified: trunk/packages/seaview/trunk/debian/manpages =================================================================== --- trunk/packages/seaview/trunk/debian/manpages 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/manpages 2009-07-07 10:41:08 UTC (rev 3589) @@ -1 +1 @@ -debian/seaview.1 +seaview.1 Deleted: trunk/packages/seaview/trunk/debian/seaview.1 =================================================================== --- trunk/packages/seaview/trunk/debian/seaview.1 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/seaview.1 2009-07-07 10:41:08 UTC (rev 3589) @@ -1,99 +0,0 @@ -.\" Title: SEAVIEW -.\" Author: Manolo Gouy <[email protected]> -.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/> -.\" Date: 05/27/2009 -.\" Manual: Seaview Manual -.\" Source: seaview 4.0 -.\" -.TH "SEAVIEW" "1" "05/27/2009" "seaview 4.0" "Seaview Manual" -.\" disable hyphenation -.nh -.\" disable justification (adjust text to left margin only) -.ad l -.SH "NAME" -seaview \- a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. -.SH "SYNOPSIS" -.HP 8 -\fBseaview\fR [\fIfilename\fR] -.SH "DESCRIPTION" -.PP -\fBseaview\fR -is the program that starts the SeaView GUI\&. -.PP -SeaView is a graphical interface for multiple sequence alignment and molecular phylogeny\&. It is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS), and allows one to manually edit the alignment, to run DOT\-PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment, and also to compute and draw phylogenetic trees\&. -.PP -If started from the command line with -\fIfilename\fR -as an argument, seaview will open the alignment stored in -\fIfilename\fR\&. -.SH "OPTIONS" -.PP -\fB\-fast\fR -.RS 4 -Suppresses double buffering for display\&. This should only accelerate display on very slow systems\&. -.RE -.PP -\fB\-fontsize\fR \fIn\fR -.RS 4 -Sets the font size to -\fIn\fR\&. -.RE -.PP -\fB\-save\fR \fIformat_name\fR -.RS 4 -Sets the default file format for saving operations\&. -\fIformat_name\fR -can be either mase, clustal, phylip, msf, fasta, or nexus\&. Without this option, SeaView autodetects the format of the opened file and uses the same for saving\&. -.RE -.SH "FILES" -.PP -\fI\fI$HOME\fR\fR\fI/\&.seaviewrc\fR -holds the user\'s configuration for SeaView\&. -.SH "SEE ALSO" -.PP -The program is fully documented online\&. Press the "help" button in the main window\&. On Debian systems, the text template for SeaView\'s help can be found in -\fI/usr/share/doc/seaview/seaview\&.html\fR\&. -.PP -Two multiple alignment programs can be called from whithin SeaView: -\fBmuscle\fR(1) -and -\fBclustalw\fR(1)\&. -.PP -The home page of SeaView is http://pbil\&.univ\-lyon1\&.fr/software/seaview\&.html\&;. -.PP -SeaView usees some components of the PHYLIP package, see \(oqhttp://evolution\&.genetics\&.washington\&.edu/phylip\&.html\(cq\&. -.SH "REFERENCE" -.PP -If you use SeaView in a published work, please cite the following reference: Galtier, N\&., Gouy, M\&. and Gautier, C\&. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny\&. Comput\&. Applic\&. Biosci\&., 12, 543\-548\&. -.SH "AUTHORS" -.PP -\fBManolo Gouy\fR <\&mg...@biomserv\&.univ\-lyon1\&.fr\&> -.sp -1n -.IP "" 4 -Upstream author of SeaView\&. -.PP -\fBStéphane Bortzmeyer\fR <\&bortzme...@debian\&.org\&> -.sp -1n -.IP "" 4 -Wrote this manpage in DocBook XML for the Debian distribution\&. -.PP -\fBCharles Plessy\fR <\&ple...@debian\&.org\&> -.sp -1n -.IP "" 4 -Updated this manpage in DocBook XML for the Debian distribution\&. -.SH "COPYRIGHT" -Copyright \(co 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Manolo Gouy -.br -Copyright \(co 1999 Stéphane Bortzmeyer -.br -Copyright \(co 2006, 2007, 2008, 2009 Charles Plessy -.br -.PP -SeaView -is released under the GNU General Public Licence, with a special permission to use some source files from the PHYLIP package\&. Because these files are used, you are not allowed generate revenue with SeaView\&. -.PP -You can redistribute and/or modify this manpage under same terms as SeaView itself\&. -.PP -On Debian systems, the complete text of the GNU General Public License version 2 can be found in -\fI/usr/share/common\-licenses/GPL\-2\fR\&. -.sp Deleted: trunk/packages/seaview/trunk/debian/seaview.1.xml =================================================================== --- trunk/packages/seaview/trunk/debian/seaview.1.xml 2009-07-07 02:02:15 UTC (rev 3588) +++ trunk/packages/seaview/trunk/debian/seaview.1.xml 2009-07-07 10:41:08 UTC (rev 3589) @@ -1,163 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<?xml-stylesheet type="text/xsl" - href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl";?> -<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" -"/usr/share/xml/docbook/schema/dtd/4.5/docbookx.dtd" [ - - <!ENTITY dhfirstname "Charles"> - <!ENTITY dhsurname "Plessy"> - <!ENTITY dhsection "1"> - <!ENTITY dhemail "[email protected]"> - <!ENTITY dhusername "&dhfirstname; &dhsurname;"> - <!ENTITY dhucpackage "SEAVIEW"> - <!ENTITY dhpackage "seaview"> - <!ENTITY dhrelease "4.0"> - <!ENTITY dhtitle "Seaview Manual"> - <!ENTITY debian "<productname>Debian</productname>"> - <!ENTITY gnu "<acronym>GNU</acronym>"> - <!ENTITY gpl "&gnu; <acronym>GPL</acronym>"> -]> - -<refentry> - <refentryinfo> - <title>&dhtitle;</title> - <productname>&dhpackage;</productname> - <releaseinfo role="version">&dhrelease;</releaseinfo> - <authorgroup> - <author> - <firstname>Manolo</firstname> - <surname>Gouy</surname> - <contrib>Upstream author of SeaView.</contrib> - <address> - <email>[email protected]</email> - </address> - </author> - <author> - <firstname>Stéphane</firstname> - <surname>Bortzmeyer</surname> - <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib> - <address> - <email>[email protected]</email> - </address> - </author> - <author> - <firstname>&dhfirstname;</firstname> - <surname>&dhsurname;</surname> - <contrib>Updated this manpage in DocBook XML for the Debian distribution.</contrib> - <address> - <email>&dhemail;</email> - </address> - </author> - </authorgroup> - <copyright> - <year>1996</year> - <year>1997</year> - <year>1998</year> - <year>1999</year> - <year>2000</year> - <year>2001</year> - <year>2002</year> - <year>2003</year> - <year>2004</year> - <year>2005</year> - <year>2006</year> - <year>2007</year> - <year>2008</year> - <year>2009</year> - <holder>Manolo Gouy</holder> - </copyright> - <copyright> - <year>1999</year> - <holder>Stéphane Bortzmeyer</holder> - </copyright> - <copyright> - <year>2006</year> - <year>2007</year> - <year>2008</year> - <year>2009</year> - <holder>Charles Plessy</holder> - </copyright> - <legalnotice> - <para><application>SeaView</application> is released under the GNU General Public Licence, with a special permission to use some source files from the PHYLIP package. Because these files are used, you are not allowed generate revenue with SeaView.</para> - - <para>You can redistribute and/or modify this manpage under same terms as SeaView itself.<!-- This also applies to this xml document. --></para> - - <para> On Debian systems, the complete text of the GNU General Public License version 2 can be found in <filename>/usr/share/common-licenses/GPL-2</filename>.</para> - </legalnotice> - </refentryinfo> - - <refmeta> - <refentrytitle>&dhucpackage;</refentrytitle> - <manvolnum>&dhsection;</manvolnum> - </refmeta> - - <refnamediv> - <refname>&dhpackage;</refname> - <refpurpose>a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.</refpurpose> - </refnamediv> - - <refsynopsisdiv> - <cmdsynopsis> - <command>&dhpackage;</command> <arg choice="opt"><replaceable>filename</replaceable></arg> - </cmdsynopsis> - </refsynopsisdiv> - - <refsect1> - <title>DESCRIPTION</title> - - <para><command>&dhpackage;</command> is the program that starts the - SeaView GUI.</para> - - <para>SeaView is a graphical interface for multiple sequence alignment and molecular phylogeny. It is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS), and allows one to manually edit the alignment, to run DOT-PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment, and also to compute and draw phylogenetic trees.</para> - - <para>If started from the command line with <filename>filename</filename> as an argument, &dhpackage; will open the alignment stored in <filename>filename</filename>.</para> - </refsect1> - - <refsect1> - <title>OPTIONS</title> - <variablelist> - <varlistentry> - <term><option>-fast</option></term> - <listitem><para>Suppresses double buffering for display. This should only accelerate display on very slow systems.</para></listitem> - </varlistentry> - - <varlistentry> - <term><option>-fontsize</option> <parameter>n</parameter></term> - <listitem><para>Sets the font size to <parameter>n</parameter>.</para></listitem> - </varlistentry> -<!-- - <varlistentry> - <term><option>-inverted</option></term> - <listitem><para>Residues will appear as black letters on a colored background</para></listitem> - </varlistentry> - --> - <varlistentry> - <term><option>-save</option> <parameter>format_name</parameter></term> - <listitem><para>Sets the default file format for saving operations. <parameter>format_name</parameter> can be either mase, clustal, phylip, msf, fasta, or nexus. Without this option, SeaView autodetects the format of the opened file and uses the same for saving.</para></listitem> - </varlistentry> - </variablelist> - </refsect1> - - <refsect1> - <title>FILES</title> - <para><filename><varname>$HOME</varname>/.seaviewrc</filename> holds the user's configuration for SeaView.</para> - </refsect1> - - <refsect1> - <title>SEE ALSO</title> - <para> The program is fully documented online. Press the "help" button in the main window. On Debian systems, the text template for SeaView's help can be found in <filename>/usr/share/doc/seaview/seaview.html</filename>.</para> - - <para> - Two multiple alignment programs can be called from whithin SeaView: <citerefentry><refentrytitle>muscle</refentrytitle><manvolnum>1</manvolnum></citerefentry> and <citerefentry><refentrytitle>clustalw</refentrytitle><manvolnum>1</manvolnum></citerefentry>. - </para> - - <para>The home page of SeaView is http://pbil.univ-lyon1.fr/software/seaview.html.</para> - - <para>SeaView usees some components of the PHYLIP package, see ‘http://evolution.genetics.washington.edu/phylip.html’.</para> - </refsect1> - - <refsect1> - <title>REFERENCE</title> - <para>If you use SeaView in a published work, please cite the following reference: Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Applic. Biosci., 12, 543-548. </para> - </refsect1> -</refentry> _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
