[med-svn] r133 - in trunk/packages/seaview/trunk/debian: . patches
Charles Plessy
charles-guest at costa.debian.org
Wed Sep 27 16:34:15 UTC 2006
Author: charles-guest
Date: 2006-09-27 16:33:58 +0000 (Wed, 27 Sep 2006)
New Revision: 133
Added:
trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.dpatch
trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.dpatch
trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch
trunk/packages/seaview/trunk/debian/seaview.1.xml
Removed:
trunk/packages/seaview/trunk/debian/patches/10-alternatives.dpatch
trunk/packages/seaview/trunk/debian/seaview.xcf
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/debian/patches/00list
trunk/packages/seaview/trunk/debian/rules
trunk/packages/seaview/trunk/debian/seaview.desktop
Log:
work on freedesktop menu, manpage, default terminal for launching muscle, and help file
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/changelog 2006-09-27 16:33:58 UTC (rev 133)
@@ -5,10 +5,12 @@
* Update debian/copyright: the current licence of seaview is GPL (Closes: #357581)
* Conforms to Standards version 3.7.2 and debhelper compatibility level 5.
* Collective maintainance: Debian-Med Packaging Team is the new Maintainer.
+ * Outputs PS instead of PDF as Debian can not support the PDFlib.
* Uses x-terminal-emulator instead of xterm.
* Support for freedesktop menus, and nice new icon.
+ * Updated manpage.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 22 Sep 2006 13:52:03 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 28 Sep 2006 01:27:27 +0900
seaview (20021127-4.1) unstable; urgency=medium
Modified: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/install 2006-09-27 16:33:58 UTC (rev 133)
@@ -1,5 +1,5 @@
-seaview seaview_align.sh usr/bin
-seaview.help usr/share/seaview
-seaview.xpm usr/share/pixmaps
-seaview.desktop usr/share/applications
-
+seaview usr/bin
+seaview_align.sh usr/share/seaview
+seaview.help usr/share/seaview
+debian/seaview.xpm usr/share/pixmaps
+debian/seaview.desktop usr/share/applications
Modified: trunk/packages/seaview/trunk/debian/patches/00list
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/00list 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/patches/00list 2006-09-27 16:33:58 UTC (rev 133)
@@ -1 +1,3 @@
-10-alternatives.dpatch
+20-no-PDF-in-help.dpatch
+21-location-of-seaview.help.dpatch
+30-align.cxx.dpatch
Deleted: trunk/packages/seaview/trunk/debian/patches/10-alternatives.dpatch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/10-alternatives.dpatch 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/patches/10-alternatives.dpatch 2006-09-27 16:33:58 UTC (rev 133)
@@ -1,48 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 10-alternatives.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
-## This patch is hereby released in public domain.
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: use x-terminal-emulator instead of xterm
-
- at DPATCH@
-
---- seaview/align.cxx 2006-09-22 13:25:47.000000000 +0900
-+++ seaview/align.cxx.patched 2006-09-22 13:48:37.000000000 +0900
-@@ -114,7 +114,8 @@
- static char *prog_path;
- static char algo_name[2][20] = {"clustalw", "muscle"};
-
--/* check for presence of xterm + clustalw/muscle + seaview_align.sh */
-+/* Modified in Debian to take advantage of the /etc/alternatives system */
-+/* check for presence of x-terminal-emulator + clustalw/muscle + seaview_align.sh */
- #ifdef WIN32
- p = (char *)(align_algorithm == CLUSTALW ? "clustalw.exe" : "muscle.exe" );
- status = check_path( p );
-@@ -144,7 +145,7 @@
- #else
- status = check_path((char*)(align_algorithm == CLUSTALW ? "clustalw" : "muscle"));
- if(status == 0) {
-- status = check_path("xterm");
-+ status = check_path("x-terminal-emulator");
- }
- if(status == 0) {
- status = check_path("seaview_align.sh");
-@@ -157,7 +158,7 @@
- #elif defined(__APPLE__)
- "program clustalw/muscle\n"
- #else
-- "one of the programs xterm, clustalw, muscle, seaview_align.sh\n"
-+ "one of the programs x-terminal-emulator, clustalw, muscle, seaview_align.sh\n"
- #endif
- "is missing");
- ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SEQS,
-@@ -249,7 +250,7 @@
- base_fname, base_fname);
- #endif
- #else
--sprintf(commande, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 "
-+sprintf(commande, "x-terminal-emulator -T \"%s alignment\" -n %s -sb -sl 2000 "
- "-e seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
- algo_name[align_algorithm]);
- l = strlen(commande);
Added: trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.dpatch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.dpatch (rev 0)
+++ trunk/packages/seaview/trunk/debian/patches/20-no-PDF-in-help.dpatch 2006-09-27 16:33:58 UTC (rev 133)
@@ -0,0 +1,21 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20-no-PDF-in-help.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Removes explanations about PDFlib in the help file, as the Debian
+## DP: version is not built against PDFlib
+
+ at DPATCH@
+
+--- seaview/seaview.help 2006-09-19 23:38:05.000000000 +0900
++++ seaview/seaview.help.debian 2006-09-25 23:08:53.000000000 +0900
+@@ -15,9 +15,6 @@
+
+ Seaview uses the FLTK project (http://www.fltk.org) for its user interface.
+
+-Seaview uses the PDFlib Lite library (http://www.pdflib.com) for pdf output
+-under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement.
+-
+ >>>Alignment panel
+ Mouse Use:
+
Added: trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.dpatch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.dpatch (rev 0)
+++ trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.dpatch 2006-09-27 16:33:58 UTC (rev 133)
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 21-location-of-seaview.help.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Set the location of seaview.help at build time
+
+ at DPATCH@
+
+--- seaview/Makefile 2006-09-19 23:38:10.000000000 +0900
++++ seaview/Makefile.debian 2006-09-25 23:25:20.000000000 +0900
+@@ -8,7 +8,7 @@
+ X11 = /usr/X11R6
+
+ #comment out and customize next line to set helpfile name at compile-time
+-#HELP_NOT_IN_PATH = -DDEFAULT_HELPFILE=\"/bge/mgouy/seaview/seaview.help\"
++HELP_NOT_IN_PATH = -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.help\"
+
+ CXX = g++
+
Property changes on: trunk/packages/seaview/trunk/debian/patches/21-location-of-seaview.help.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch (rev 0)
+++ trunk/packages/seaview/trunk/debian/patches/30-align.cxx.dpatch 2006-09-27 16:33:58 UTC (rev 133)
@@ -0,0 +1,56 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 30-align.cxx.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Use the Debian alternatives system ; hardocode the location of the
+## DP: helper file
+
+ at DPATCH@
+
+--- seaview/align.cxx 2006-09-25 23:41:13.000000000 +0900
++++ seaview/align.cxx.debian 2006-09-25 23:42:26.000000000 +0900
+@@ -114,7 +114,8 @@
+ static char *prog_path;
+ static char algo_name[2][20] = {"clustalw", "muscle"};
+
+-/* check for presence of xterm + clustalw/muscle + seaview_align.sh */
++/* Modified in Debian to take advantage of the /etc/alternatives system */
++/* check for presence of x-terminal-emulator + clustalw/muscle + seaview_align.sh */
+ #ifdef WIN32
+ p = (char *)(align_algorithm == CLUSTALW ? "clustalw.exe" : "muscle.exe" );
+ status = check_path( p );
+@@ -144,11 +145,12 @@
+ #else
+ status = check_path((char*)(align_algorithm == CLUSTALW ? "clustalw" : "muscle"));
+ if(status == 0) {
+- status = check_path("xterm");
++ status = check_path("x-terminal-emulator");
+ }
+- if(status == 0) {
++/* if(status == 0) {
+ status = check_path("seaview_align.sh");
+ }
++*/
+ #endif
+ if(status != 0) {
+ fl_message("Alignment operation is impossible because\n"
+@@ -157,7 +159,7 @@
+ #elif defined(__APPLE__)
+ "program clustalw/muscle\n"
+ #else
+- "one of the programs xterm, clustalw, muscle, seaview_align.sh\n"
++ "one of the programs x-terminal-emulator, clustalw, muscle, seaview_align.sh\n"
+ #endif
+ "is missing");
+ ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SEQS,
+@@ -249,8 +251,8 @@
+ base_fname, base_fname);
+ #endif
+ #else
+-sprintf(commande, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 "
+- "-e seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
++sprintf(commande, "x-terminal-emulator -T \"%s alignment\" -n %s -sb -sl 2000 "
++ "-e /usr/share/seaview/seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
+ algo_name[align_algorithm]);
+ l = strlen(commande);
+ switch (align_algorithm) {
Modified: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/rules 2006-09-27 16:33:58 UTC (rev 133)
@@ -9,6 +9,8 @@
DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+PROGRAM_NAME = seaview
+
CFLAGS+=-Wall
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
@@ -27,15 +29,16 @@
dpatch deapply-all
rm -rf patch-stamp debian/patched
-build: patch build-stamp
+build: patch build-stamp debian/$(PROGRAM_NAME).1
build-stamp:
dh_testdir
-
- # Add here commands to compile the package.
$(MAKE) OPT="$(CFLAGS)" seaviewps
-
touch build-stamp
+
+debian/$(PROGRAM_NAME).1: debian/$(PROGRAM_NAME).1.xml
+ xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl debian/$(PROGRAM_NAME).1.xml
+
clean: clean-patched unpatch
clean-patched:
@@ -43,7 +46,7 @@
dh_testroot
rm -f build-stamp
rm -f *.o seaview
- dh_clean
+ dh_clean debian/$(PROGRAM_NAME).1
install: build
dh_testdir
@@ -60,10 +63,10 @@
dh_testroot
dh_installchangelogs
dh_installdocs
- dh_installexamples examples/*
+ dh_installexamples examples/* protein.mase
dh_installmenu
-# dh_desktop
- dh_installman seaview.1
+ dh_desktop
+ dh_installman debian/seaview.1
dh_strip
dh_compress
dh_fixperms
Added: trunk/packages/seaview/trunk/debian/seaview.1.xml
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.1.xml (rev 0)
+++ trunk/packages/seaview/trunk/debian/seaview.1.xml 2006-09-27 16:33:58 UTC (rev 133)
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>2006-09-27</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>SEAVIEW</refentrytitle>">
+ <!ENTITY dhpackage "seaview">
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+<!-- <author>
+ &dhfirstname;
+ &dhsurname;
+ </author> -->
+ <copyright>
+ <year>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>a multiple sequence alignment editor</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 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 or CLUSTAL programs to locally improve the alignment.</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>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 home page of SeaView is pbil.univ-lyon1.fr/software/seaview.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>
+
+ <refsect1>
+ <title>AUTHORS</title>
+
+ <para><application>SeaView</application> is Copyright (C) 1996-2005 Manolo Gouy <email>mgouy at biomserv.univ-lyon1.fr</email>. It is released under the GNU General Public Licence</para>
+
+ <para>This manual page was written by Stephane Bortzmeyer <email>bortzmeyer at debian.org</email> and updated by &dhusername; (&dhemail;) for the &debian; system (but may be used by others). You can redistribute it and/or modify it under the terms of the GNU General Public License.<!-- This also applies to this xml document. --></para>
+
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
Modified: trunk/packages/seaview/trunk/debian/seaview.desktop
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.desktop 2006-09-26 09:14:06 UTC (rev 132)
+++ trunk/packages/seaview/trunk/debian/seaview.desktop 2006-09-27 16:33:58 UTC (rev 133)
@@ -8,11 +8,12 @@
GenericName=Multiple sequence alignment editor
GenericName[en]=Multiple sequence alignment editor
GenericName[fr]=Éditeur d'alignements multiples de séquences
-GenericName[pt_BR]=
+GenericName[pt_BR]=Editor de alinhamento múltiplo de seqüências
Comment=Edits multiple sequence alignments and prints them in PostScript format.
Comment[en]=Edits multiple sequence alignments and prints them in PostScript format.
Comment[fr]=Édite des aligmements multiples de séquences et les imprime au format PostScript.
-Comment[pt_BR]=
+Comment[pt_BR]=Edita múltiplos alinhamentos de seqüências e os imprimem em formato PostScript.
Type=Application
Categories=Biology;Science;Education;
+
Deleted: trunk/packages/seaview/trunk/debian/seaview.xcf
===================================================================
(Binary files differ)
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