[med-svn] r135 - in trunk/packages/seaview/trunk: . debian

[Charles Plessy]

Author: charles-guest
Date: 2006-09-28 06:23:57 +0000 (Thu, 28 Sep 2006)
New Revision: 135

Added:
   trunk/packages/seaview/trunk/debian/README.Debian
Removed:
   trunk/packages/seaview/trunk/seaview.1
Modified:
   trunk/packages/seaview/trunk/debian/changelog
   trunk/packages/seaview/trunk/debian/control
   trunk/packages/seaview/trunk/debian/menu
   trunk/packages/seaview/trunk/debian/rules
Log:
missing dependancies and build rules, tidying

Added: trunk/packages/seaview/trunk/debian/README.Debian
===================================================================
--- trunk/packages/seaview/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/seaview/trunk/debian/README.Debian	2006-09-28 06:23:57 UTC (rev 135)
@@ -0,0 +1,18 @@
+SeaView for Debian
+------------------
+
+The version of SeaView packaged for Debian has the following modifications:
+
+- It uses by default the program "Muscle" for re-aligning residues, as ClustalW
+  is not free enough to be distributed in Debian.
+
+- It outputs the alignments in PostScript format and not in PDF, as the
+  software for PDF support (PDFlib) is not free enough to be distributed in
+  Debian.
+
+- It uses the default X terminal emulator instead of Xterm, when re-aligning
+  residues. You can check which alternative you are using with the following
+  command:
+    /usr/sbin/update-alternatives --display x-terminal-emulator
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 28 Sep 2006 12:13:53 +0900

Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog	2006-09-28 01:54:13 UTC (rev 134)
+++ trunk/packages/seaview/trunk/debian/changelog	2006-09-28 06:23:57 UTC (rev 135)
@@ -8,9 +8,9 @@
   * 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. 
+  * Updated manpage.
 
- -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 28 Sep 2006 01:27:27 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Thu, 28 Sep 2006 12:13:53 +0900
 
 seaview (20021127-4.1) unstable; urgency=medium
 

Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control	2006-09-28 01:54:13 UTC (rev 134)
+++ trunk/packages/seaview/trunk/debian/control	2006-09-28 06:23:57 UTC (rev 135)
@@ -3,7 +3,7 @@
 Priority: optional
 Maintainer: Debian-Med Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
 Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper ( >= 5  ), libfltk1.1-dev, dpatch
+Build-Depends: debhelper ( >= 5  ), libfltk1.1-dev, dpatch, xsltproc, docbook-xsl, docbook-xml
 Standards-Version: 3.7.2
 
 Package: seaview
@@ -11,7 +11,7 @@
 Depends: ${shlibs:Depends}
 Recommends: muscle, xterm | x-terminal-emulator
 Description: [Biology] Multiple sequence alignment editor
- SeaView is a graphical multiple sequence alignment editor developped by Manolo
+ SeaView is a graphical multiple sequence alignment editor developed by Manolo
  Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF,
  CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and
  also to run DOT-PLOT or MUSCLE programs to locally improve the alignment.

Modified: trunk/packages/seaview/trunk/debian/menu
===================================================================
--- trunk/packages/seaview/trunk/debian/menu	2006-09-28 01:54:13 UTC (rev 134)
+++ trunk/packages/seaview/trunk/debian/menu	2006-09-28 06:23:57 UTC (rev 135)
@@ -1,7 +1,8 @@
 ?package(seaview):\
- needs=x11\
- section=Apps/Science\
- hints=Biology\
- longtitle="SeaView: multiple sequence alignment editor"\
- title=SeaView\
- command=seaview
+	needs="X11"\
+	section="Apps/Science"\
+	hints="Multiple sequence alignment"\
+	longtitle="SeaView: multiple sequence alignment editor"\
+	title="SeaView"\
+	command="/usr/bin/seaview"\
+	icon="/usr/share/pixmaps/seaview.xpm"

Modified: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules	2006-09-28 01:54:13 UTC (rev 134)
+++ trunk/packages/seaview/trunk/debian/rules	2006-09-28 06:23:57 UTC (rev 135)
@@ -76,5 +76,7 @@
 	dh_md5sums
 	dh_builddeb
 
+binary-indep:
+
 binary: binary-indep binary-arch
 .PHONY: build clean binary-indep binary-arch binary install

Deleted: trunk/packages/seaview/trunk/seaview.1
===================================================================
--- trunk/packages/seaview/trunk/seaview.1	2006-09-28 01:54:13 UTC (rev 134)
+++ trunk/packages/seaview/trunk/seaview.1	2006-09-28 06:23:57 UTC (rev 135)
@@ -1,43 +0,0 @@
-.TH SEAVIEW 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
-seaview \- a multiple sequence alignment editor
-.SH SYNOPSIS
-.B seaview
-.I "[options] [filename]"
-.SH "DESCRIPTION"
-This manual page documents briefly the
-.BR seaview ,
-command.
-This manual page was written for the Debian GNU/Linux distribution
-because the original program does not have a manual page.
-Instead, it has online documentation, see below.
-.PP
-.B 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.
-.SH OPTIONS
-.TP
-.B \-save <format_name>
-format_name, either mase, clustal, phylip, msf, fasta, or nexus, sets the 
-default file format for saving operations
-.TP
-.B \-fast
-sequences will be displayed faster but less smoothly
-.TP
-.B \-inverted
-residues will appear as black letters on a colored background
-.SH ARGUMENT
-"filename"
-is an optional alignment file to be loaded. The expected format for this file
-is that of the default format for saving operations.
-.SH "SEE ALSO"
-The program is fully documented online. Press the "help" button in the
-main window.
-.SH AUTHOR
-This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
-for the Debian GNU/Linux system (but may be used by others).