[med-svn] r770 - trunk/packages/seaview/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Thu Nov 8 02:03:56 UTC 2007
Author: charles-guest
Date: 2007-11-08 02:03:55 +0000 (Thu, 08 Nov 2007)
New Revision: 770
Added:
trunk/packages/seaview/trunk/debian/seaview.1
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/control
trunk/packages/seaview/trunk/debian/rules
Log:
Building manpage offline and updating Vcs fields.
* Removed the XS- prefix of the Vcs fields in debian/control
* Building the manpage offline: added seaview.1 to the package, and
removed xsltproc, docbook-xml and docbook-xsl from the build-dependencies.
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2007-11-07 22:00:41 UTC (rev 769)
+++ trunk/packages/seaview/trunk/debian/changelog 2007-11-08 02:03:55 UTC (rev 770)
@@ -1,4 +1,4 @@
-seaview (1:2.1-1) unstable; urgency=low
+seaview (1:2.2-1) unstable; urgency=low
[ Nelson A. de Oliveira ]
* Updated watch file.
@@ -6,8 +6,11 @@
[ Charles Plessy ]
* Moved the Homepage: field out from the package's description.
* New upstream release: introduced interface to external alignment programs.
+ * Removed the XS- prefix of the Vcs fields in debian/control
+ * Building the manpage offline: added seaview.1 to the package, and
+ removed xsltproc, docbook-xml and docbook-xsl from the build-dependencies.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 23 Sep 2007 10:01:09 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 08 Nov 2007 10:59:35 +0900
seaview (1:2.0-1) unstable; urgency=low
Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control 2007-11-07 22:00:41 UTC (rev 769)
+++ trunk/packages/seaview/trunk/debian/control 2007-11-08 02:03:55 UTC (rev 770)
@@ -3,10 +3,10 @@
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper ( >= 5 ), libfltk1.1-dev, quilt, xsltproc, docbook-xsl, docbook-xml
+Build-Depends: debhelper ( >= 5 ), libfltk1.1-dev, quilt
Standards-Version: 3.7.2
-XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seaview/trunk/
-XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seaview
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seaview/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seaview
Homepage: http://pbil.univ-lyon1.fr/software/seaview.html
Package: seaview
Modified: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules 2007-11-07 22:00:41 UTC (rev 769)
+++ trunk/packages/seaview/trunk/debian/rules 2007-11-08 02:03:55 UTC (rev 770)
@@ -23,20 +23,12 @@
include /usr/share/quilt/quilt.make
-build: patch build-stamp debian/$(PROGRAM_NAME).1
+build: patch build-stamp
build-stamp:
dh_testdir
$(MAKE) OPT="$(CFLAGS)" seaviewps
touch build-stamp
-debian/$(PROGRAM_NAME).1: debian/$(PROGRAM_NAME).1.xml
- xsltproc -o debian/ \
- -''-nonet \
- -''-param man.charmap.use.subset "0" \
- -''-param make.year.ranges "1" \
- -''-param make.single.year.ranges "1" \
- debian/$(PROGRAM_NAME).1.xml
-
clean: clean-patched unpatch
clean-patched:
@@ -44,15 +36,12 @@
dh_testroot
rm -f build-stamp
rm -f *.o seaview
- dh_clean debian/$(PROGRAM_NAME).1
install: build
dh_testdir
- dh_testroot
+ dh_testroot
dh_clean -k
dh_installdirs
-
- # Add here commands to install the package into debian/<packagename>
dh_install
# Build architecture-dependent files here.
Added: trunk/packages/seaview/trunk/debian/seaview.1
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1 (rev 0)
+++ trunk/packages/seaview/trunk/debian/seaview.1 2007-11-08 02:03:55 UTC (rev 770)
@@ -0,0 +1,103 @@
+.\" Title: SEAVIEW
+.\" Author: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 11/08/2007
+.\" Manual: Seaview Manual
+.\" Source: seaview 20070615
+.\"
+.TH "SEAVIEW" "1" "11/08/2007" "seaview 20070615" "Seaview Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+seaview \- a multiple sequence alignment editor
+.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 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.
+.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\-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.
+\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/seaview/seaview.help\fR
+(It is human readable).
+.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.
+.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 <\&mgouy at biomserv.univ\-lyon1.fr\&>
+.sp -1n
+.IP "" 4
+Upstream author of SeaView.
+.PP
+\fBStéphane Bortzmeyer\fR <\&bortzmeyer at debian.org\&>
+.sp -1n
+.IP "" 4
+Wrote this manpage in DocBook XML for the Debian distribution.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy.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 Manolo Gouy
+.br
+Copyright \(co 1999 Stéphane Bortzmeyer
+.br
+Copyright \(co 2006, 2007 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.
+.PP
+On Debian systems, the complete text of the GNU General Public License can be found in
+\fI/usr/share/common\-licenses/GPL\fR.
+.br
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