Author: plessy
Date: 2009-05-17 00:19:41 +0000 (Sun, 17 May 2009)
New Revision: 3383
Added:
trunk/packages/seaview/trunk/debian/docs
trunk/packages/seaview/trunk/debian/manpages
trunk/packages/seaview/trunk/debian/seaview.doc-base.help
trunk/packages/seaview/trunk/debian/seaview.examples
Removed:
trunk/packages/seaview/trunk/debian/README.source
trunk/packages/seaview/trunk/debian/patches/
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/control
trunk/packages/seaview/trunk/debian/copyright
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/debian/rules
trunk/packages/seaview/trunk/debian/seaview.1
trunk/packages/seaview/trunk/debian/seaview.1.xml
Log:
Ready for upload now that phyml is in Debian.
- Recommends phyml and muscle.
- Dropped dependancy on xterm.
- Updated description and removed reference from it.
- debian/README.source removed:
- corrected DHELPFILENAME=\\\"/usr/share/doc/seaview/seaview.html\\\"
- Uses `dh binary-arch` in the binary-arch targed (created debian/docs,
debian/seaview.examples, and debian/manpages).
- Updated the manpage (debian/seaview.1*).
- Registered the new help file with doc-base (debian/seaview.doc-base.help).
Deleted: trunk/packages/seaview/trunk/debian/README.source
===================================================================
--- trunk/packages/seaview/trunk/debian/README.source 2009-05-16 06:47:48 UTC
(rev 3382)
+++ trunk/packages/seaview/trunk/debian/README.source 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -1,3 +0,0 @@
-The upstream sources are patched using the quilt program during the building of
-the Debian binary package. Please refer to /usr/share/doc/quilt/README.source
-for more instructions.
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2009-05-16 06:47:48 UTC
(rev 3382)
+++ trunk/packages/seaview/trunk/debian/changelog 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -1,16 +1,14 @@
seaview (1:4.0-1) UNRELEASED; urgency=low
- TODO: add new debtags (download, phylogeny, …)
- rewrite description.
- Debdiff, update manpage if necessary, document changes.
-
- * New upstream version.
+ * New upstream version that computes and draws parsimony, distance and PhyML
+ phylogenetic trees.
* debian/control:
- - Recommends Phyml.
+ - Recommends phyml and muscle.
+ - Dropped dependancy on xterm.
- checked package conformance with Policy 3.8.1.
- - Removed reference from description.
+ - Updated description and removed reference from it.
- Dropped build dependency on quilt.
- * debian/patches removed:
+ * debian/patches and debian/README.source removed:
- 20-no-PDF-in-help.patch: upstream wording became true for Debian as well.
- 21-location-of-seaview.help.patch: passing -DHELPFILENAME through
debian/rules instead.
@@ -20,14 +18,18 @@
- Makes `seaview' instead of `seaviewps' as (non-free) PDF support is not
default anymore.
- Indicate the location of the help file with:
- -DHELPFILENAME=\\\"/usr/share/njplot/njplot.help\\\"
+ -DHELPFILENAME=\\\"/usr/share/doc/seaview/seaview.html\\\"
- Uses `dh clean' and $(RM) macro in the clean target.
+ - Uses `dh binary-arch` in the binary-arch targed (created debian/docs,
+ debian/seaview.examples, and debian/manpages).
- Removed protein.mase from examples (removed upstream).
- Removed patching facilities (no patches to apply anymore).
* Removed `seaview_align.sh' from debian/install, as it was removed upstream.
* debian/copyright:
- Incremented year and version.
- Link to the precise versions of the GNU GPL and LGPL.
+ * Updated the manpage (debian/seaview.1*).
+ * Registered the new help file with doc-base (debian/seaview.doc-base.help).
-- Charles Plessy <[email protected]> Mon, 16 Mar 2009 13:18:29 +0900
Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control 2009-05-16 06:47:48 UTC (rev
3382)
+++ trunk/packages/seaview/trunk/debian/control 2009-05-17 00:19:41 UTC (rev
3383)
@@ -13,11 +13,16 @@
Package: seaview
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: xterm, phyml
-Suggests: muscle, clustalw
-Description: Multiple sequence alignment editor
- SeaView is a graphical multiple sequence alignment editor developed by Manolo
- Gouy. Multiple alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE)
- are supported for reading and writing. Alignments can be manually edited.
- The user is further supported by an integration of external programs,
- i.e., to run DOT-PLOT or MUSCLE, to locally improve the alignment.
+Recommends: muscle, phyml
+Suggests: clustalw
+Description: Multiplatform interface for sequence alignment and phylogeny
+ SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
+ PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
+ Alignments can be manually edited. It drives the programs Muscle or Clustal W
+ for multiple sequence alignment, and also allows to use any external alignment
+ algorithm able to read and write FASTA-formatted files. It computes
+ phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by
+ distance with NJ or BioNJ algorithms on a variety of evolutionary distances,
or
+ by maximum likelihood using the program PhyML 3.0. SeaView draws phylogenetic
+ trees on screen or PostScript files, and allows to download sequences from
+ EMBL/GenBank/UniProt using the Internet.
Modified: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright 2009-05-16 06:47:48 UTC
(rev 3382)
+++ trunk/packages/seaview/trunk/debian/copyright 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -1,13 +1,11 @@
-Format-Specification:
http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=402
-Upstream-Name: SeaView
-Upstream-Maintainer: Manolo Gouy <[email protected]>
-Upstream-Source:
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.0.tar.gz
-X-Packaged-By: Stephane Bortzmeyer <[email protected]>
-X-Packaged-Date: Mon, 1 Mar 1999 16:41:51 +0100
+Format: 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
-Files: *
-Copyright: © 1996-2009 Manolo Gouy <[email protected]>
-X-Comment: If you use SeaView in a published work, please cite the following
reference:
+Copyright: 1996-2009 Manolo Gouy <[email protected]>
+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.
@@ -25,7 +23,7 @@
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-X-Comment: On Debian systems, the complete text of the GNU General
+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'.
Files: FL/*
@@ -45,7 +43,7 @@
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
-X-Comment: On Debian systems, the complete text of the GNU Lesser General
+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'.
Files: debian/*
Added: trunk/packages/seaview/trunk/debian/docs
===================================================================
--- trunk/packages/seaview/trunk/debian/docs (rev 0)
+++ trunk/packages/seaview/trunk/debian/docs 2009-05-17 00:19:41 UTC (rev
3383)
@@ -0,0 +1,2 @@
+seaview.html
+debian/references
Modified: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install 2009-05-16 06:47:48 UTC (rev
3382)
+++ trunk/packages/seaview/trunk/debian/install 2009-05-17 00:19:41 UTC (rev
3383)
@@ -1,5 +1,4 @@
seaview usr/bin
-seaview.help usr/share/seaview
seaview.xpm usr/share/pixmaps
debian/seaview.desktop usr/share/applications
debian/seaview.svg usr/share/icons/hicolor/scalable/apps
Added: trunk/packages/seaview/trunk/debian/manpages
===================================================================
--- trunk/packages/seaview/trunk/debian/manpages
(rev 0)
+++ trunk/packages/seaview/trunk/debian/manpages 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -0,0 +1 @@
+debian/seaview.1
Modified: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules 2009-05-16 06:47:48 UTC (rev
3382)
+++ trunk/packages/seaview/trunk/debian/rules 2009-05-17 00:19:41 UTC (rev
3383)
@@ -24,10 +24,10 @@
build: build-stamp
build-stamp:
dh_testdir
- $(MAKE) OPT="$(CFLAGS) \
- -DPHYMLNAME=\\\"phyml\\\" \
- -DDEFAULT_HELPFILE=\\\"/usr/share/seaview/seaview.help\\\"" \
- $(PROGRAM_NAME) \
+ $(MAKE) OPT="$(CFLAGS)
\
+ -DPHYMLNAME=\\\"phyml\\\"
\
+ -DDEFAULT_HELPFILE=\\\"/usr/share/doc/seaview/seaview.html\\\""
\
+ $(PROGRAM_NAME)
\
PNGJPEGLIBS='-lpng -ljpeg' FLTKLIBS='-lfltk -lfltk_images'
touch build-stamp
@@ -41,23 +41,7 @@
# Build architecture-dependent files here.
binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs debian/references
- dh_installexamples debian/examples/*
- dh_installmenu
- dh_desktop
- dh_installmime
- dh_installman debian/seaview.1
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
+ dh binary-arch
binary-indep:
Modified: trunk/packages/seaview/trunk/debian/seaview.1
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1 2009-05-16 06:47:48 UTC
(rev 3382)
+++ trunk/packages/seaview/trunk/debian/seaview.1 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -1,103 +1,97 @@
.\" Title: SEAVIEW
.\" Author: Manolo Gouy <[email protected]>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 03/05/2008
+.\" Date: 05/17/2009
.\" Manual: Seaview Manual
-.\" Source: seaview 2.4
+.\" Source: seaview 4.0
.\"
-.TH "SEAVIEW" "1" "03/05/2008" "seaview 2.4" "Seaview Manual"
+.TH "SEAVIEW" "1" "05/17/2009" "seaview 4.0" "Seaview Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-seaview - a multiple sequence alignment editor
+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\.
+is the program that starts the SeaView GUI\&.
.PP
-SeaView is a graphical multiple sequence alignment editor\. SeaView is able to
read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS)\. It
allows one to manually edit the alignment, and also to run DOT\-PLOT, CLUSTAL
or MUSCLE programs to locally improve the alignment\.
+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\.
+\fIfilename\fR\&.
.SH "OPTIONS"
.PP
\fB\-fast\fR
.RS 4
-Suppresses double buffering for display\. This should only accelerate display
on very slow systems\.
+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\.
+\fIn\fR\&.
.RE
.PP
-\fB\-inverted\fR
-.RS 4
-Residues will appear as black letters on a colored background
-.RE
-.PP
\fB\-save\fR \fIformat_name\fR
.RS 4
-Sets the default file format for saving operations\.
+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\.
+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\.
+\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/seaview/seaview\.help\fR
-(It is human readable)\.
+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)\.
+\fBclustalw\fR(1)\&.
.PP
-The home page of SeaView is
http://pbil\.univ\-lyon1\.fr/software/seaview\.html\.
+The home page of SeaView is
http://pbil\&.univ\-lyon1\&.fr/software/seaview\&.html\&;.
.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\.
+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\&>
+\fBManolo Gouy\fR <\&mg...@biomserv\&.univ\-lyon1\&.fr\&>
.sp -1n
.IP "" 4
-Upstream author of SeaView\.
+Upstream author of SeaView\&.
.PP
-\fBStéphane Bortzmeyer\fR <\&bortzme...@debian\.org\&>
+\fBStéphane Bortzmeyer\fR <\&bortzme...@debian\&.org\&>
.sp -1n
.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution\.
+Wrote this manpage in DocBook XML for the Debian distribution\&.
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nos...@plessy\.org\&>
+\fBCharles Plessy\fR <\&ple...@debian\&.org\&>
.sp -1n
.IP "" 4
-Updated this manpage in DocBook XML for the Debian distribution\.
+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 Manolo Gouy
+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 Charles Plessy
+Copyright \(co 2006, 2007, 2008, 2009 Charles Plessy
.br
.PP
SeaView
is released under the GNU General Public Licence
.PP
-You can redistribute and/or modify this manpage under same terms as SeaView
itself\.
+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 can be
found in
-\fI/usr/share/common\-licenses/GPL\fR\.
+\fI/usr/share/common\-licenses/GPL\fR\&.
.sp
Modified: trunk/packages/seaview/trunk/debian/seaview.1.xml
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1.xml 2009-05-16 06:47:48 UTC
(rev 3382)
+++ trunk/packages/seaview/trunk/debian/seaview.1.xml 2009-05-17 00:19:41 UTC
(rev 3383)
@@ -1,17 +1,17 @@
<?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 V4.4//EN"
-"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+<!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 dhemail "[email protected]">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhucpackage "SEAVIEW">
<!ENTITY dhpackage "seaview">
- <!ENTITY dhrelease "2.4">
+ <!ENTITY dhrelease "4.0">
<!ENTITY dhtitle "Seaview Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
@@ -63,6 +63,7 @@
<year>2006</year>
<year>2007</year>
<year>2008</year>
+ <year>2009</year>
<holder>Manolo Gouy</holder>
</copyright>
<copyright>
@@ -73,6 +74,7 @@
<year>2006</year>
<year>2007</year>
<year>2008</year>
+ <year>2009</year>
<holder>Charles Plessy</holder>
</copyright>
<legalnotice>
@@ -91,7 +93,7 @@
<refnamediv>
<refname>&dhpackage;</refname>
- <refpurpose>a multiple sequence alignment editor</refpurpose>
+ <refpurpose>a multiplatform, graphical user interface for multiple
sequence alignment and molecular phylogeny.</refpurpose>
</refnamediv>
<refsynopsisdiv>
@@ -106,7 +108,7 @@
<para><command>&dhpackage;</command> is the program that starts the
SeaView GUI.</para>
- <para>SeaView is a graphical multiple sequence alignment editor. SeaView
is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE,
NEXUS). It allows one to manually edit the alignment, and also to run
DOT-PLOT, CLUSTAL or MUSCLE programs to locally improve the alignment.</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>
@@ -123,12 +125,12 @@
<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>
@@ -143,7 +145,7 @@
<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/seaview/seaview.help</filename> (It is human
readable).</para>
+ <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>.
Added: trunk/packages/seaview/trunk/debian/seaview.doc-base.help
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.doc-base.help
(rev 0)
+++ trunk/packages/seaview/trunk/debian/seaview.doc-base.help 2009-05-17
00:19:41 UTC (rev 3383)
@@ -0,0 +1,8 @@
+Document: seaview-help
+Title: SeaView help
+Author: Manolo Gouy <[email protected]>
+Abstract: This is the hypertext help available when running SeaView.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/seaview/seaview.html
Added: trunk/packages/seaview/trunk/debian/seaview.examples
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.examples
(rev 0)
+++ trunk/packages/seaview/trunk/debian/seaview.examples 2009-05-17
00:19:41 UTC (rev 3383)
@@ -0,0 +1 @@
+debian/examples/*
_______________________________________________
debian-med-commit mailing list
[email protected]
http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
