[med-svn] r217 - trunk/packages/boxshade/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Feb 24 04:42:37 CET 2007
Author: charles-guest
Date: 2007-02-24 04:42:36 +0100 (Sat, 24 Feb 2007)
New Revision: 217
Removed:
trunk/packages/boxshade/trunk/debian/conffiles
trunk/packages/boxshade/trunk/debian/dirs
trunk/packages/boxshade/trunk/debian/install
Modified:
trunk/packages/boxshade/trunk/debian/boxshade.1.xml
trunk/packages/boxshade/trunk/debian/changelog
trunk/packages/boxshade/trunk/debian/control
trunk/packages/boxshade/trunk/debian/copyright
trunk/packages/boxshade/trunk/debian/rules
Log:
updating and relicencing the manpage, fixing build, updating debian/control, closing bug.
Modified: trunk/packages/boxshade/trunk/debian/boxshade.1.xml
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.1.xml 2007-02-21 00:08:48 UTC (rev 216)
+++ trunk/packages/boxshade/trunk/debian/boxshade.1.xml 2007-02-24 03:42:36 UTC (rev 217)
@@ -1,44 +1,28 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
-"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
+<?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"
+"http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
-<!--
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
-Process this file with an XSLT processor: `xsltproc \
--''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl manpage.dbk'. A manual page
-<package>.<section> will be generated. You may view the
-manual page with: nroff -man <package>.<section> | less'. A
-typical entry in a Makefile or Makefile.am is:
-
-DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
-manpages/docbook.xsl
-XP=xsltproc -''-nonet
-
-manpage.1: manpage.dbk
- $(XP) $(DB2MAN) $<
-
-The xsltproc binary is found in the xsltproc package. The
-XSL files are in docbook-xsl. Please remember that if you
-create the nroff version in one of the debian/rules file
-targets (such as build), you will need to include xsltproc
-and docbook-xsl in your Build-Depends control field.
-
--->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>February 26, 2004</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
+ <!ENTITY dhdate "February 23, 2007">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhemail "<email>steffen_moeller at gmx.de</email>">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>BOXSHADE</refentrytitle>">
<!ENTITY dhpackage "boxshade">
-
+ <!ENTITY dhrelease "3.3">
+ <!ENTITY dhtitle "Boxshade Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -46,24 +30,110 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Kay</firstname>
+ <surname>Hofmann</surname>
+ <affiliation>
+ <orgname>ISREC</orgname>
+ <orgdiv>Bioinformatics Group</orgdiv>
+ <address>
+ <postcode>CH-1066</postcode>
+ <city>Epalinges s/Lausanne</city> <country>Switzerland</country>
+ </address>
+ </affiliation>
+ <contrib>Wrote Boxshade.</contrib>
+ <email>kay.hofmann at memorec.com</email>
+ </author>
+ <author>
+ <firstname>Michael</firstname>
+ <firstname>D</firstname>
+ <surname>Baron</surname>
+ <affiliation>
+ <orgname>BBSRC Institute for Animal Health</orgname>
+ <address>
+ <city>Pirbright</city>,
+ <state>Surrey</state>
+ <postcode>GU24 0NF</postcode>
+ <country>U.K.</country>
+ </address>
+ </affiliation>
+ <contrib>Wrote Boxshade.</contrib>
+ <email>michael.baron at bbsrc.ac.uk</email>
+ </author>
+ <author>
+ <firstname>Harmut</firstname>
+ <surname>Schirmer</surname>
+ <affiliation>
+ <orgname>Technische Fakultaet</orgname>
+ <address>
+ <street>Kaiserstr. 2</street>
+ <postcode>D-24143</postcode>
+ <city>Kiel</city>
+ <country>Germany</country>
+ </address>
+ </affiliation>
+ <contrib>
+ C port of Boxshade. (don't send Kay or Michael any questions concerning the 'C' version of boxshade)
+ </contrib>
+ <email>hsc at techfak.uni-kiel.de</email>
+ </author>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ <contrib>
+ Wrote the manpage.
+ </contrib>
+ <address>
+ &dhemail;
+ </address>
+ </author>
+ <author>
+ <firstname>Charles</firstname>
+ <surname>Plessy</surname>
+ <contrib>
+ Updated the manpage
+ </contrib>
+ <address>
+ <email>
+ charles-debian-nospam at plessy.org
+ </email>
+ </address>
+ </author>
+ </authorgroup>
<copyright>
+ <year>1997</year>
+ <holder>Kay Hofmann, Michael Baron and Harmut Schirmer</holder>
+ </copyright>
+ <copyright>
<year>2003</year>
+ <year>2007</year>
<holder>&dhusername;</holder>
+ <holder>Charles Plessy</holder>
</copyright>
- &dhdate;
+ <legalnotice>
+ <para>
+ The above copyright notices refer to the program and its manpage respectively.
+ </para>
+ <para>
+ BOXSHADE is completely public-domain and may be passed around and modified without any notice to the authors.
+ </para>
+ <para>
+ This manual page was written for the &debian; system but may be used by others. Permission is granted to copy, distribute and/or modify this document under same terms as &dhpackage; itself.
+ </para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
+
<refnamediv>
<refname>&dhpackage;</refname>
@@ -98,7 +168,8 @@
with parameters from the command line. At the moment, the VMS and DOS
versions of BOXSHADE have identical user interfaces.
</para>
-<para>- Input formats -</para>
+ <refsect2>
+ <title>Input formats</title>
<para>
BOXSHADE 3.2 knows about the following input file formats: (some of
the are generally used only for MSDOS or VMS systems) + CLUSTAL and
@@ -114,7 +185,10 @@
file type from the extension but will work also if different extensions
are used.
</para>
-<para> - Output devices - </para>
+</refsect2>
+
+<refsect2>
+ <title>Output devices</title>
<para>POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on
a Laserprinter or for further conversion with a POSTCRIPT interpreter
(like GHOSTSCRIPT) + HPGL for export to various graphics programs or
@@ -146,7 +220,10 @@
as output device, the 'RETURN' key has to be pressed to obtain the next
page of output.
</para>
-<para>- Sequence numbering - </para>
+</refsect2>
+
+<refsect2>
+ <title>Sequence numbering</title>
<para>Starting with version 2.2 there
is the possibility to add numbering to the output files. The numbers are
printed between the sequence names and the sequence itself. Since most of
@@ -159,7 +236,10 @@
position and continues numbering every valid symbol, skipping blanks,
'-','.' and stuff like that.
</para>
-<para>- Default parameters -</para>
+</refsect2>
+
+<refsect2>
+<title>Default parameters</title>
<para>Several people using
previous releases of BOXSHADE pointed me to the need of having default
parameters for the various questions asked by the program. They argued
@@ -195,10 +275,13 @@
use out=con: on VMS machines, use out=tt: note2: if no mode is specified,
the native style of the machine is used.
</para>
-<para>ATTENTION</para>
-<para>on unix systems, the dash (-) instead of the slash (/) has to be used as separation character for command line paramters. For example, a valid unix command line is: <command>boxshade -def -numdef -cons -symbcons=" .*" **************************************************************************</command>
-</para>
-<para>- Shading strategies (similarity to consensus or single sequence) -</para>
+<note><title>ATTENTION</title>
+<para>on unix systems, the dash (-) instead of the slash (/) has to be used as separation character for command line paramters. For example, a valid unix command line is: <command>boxshade -def -numdef -cons -symbcons=" .*"</command>
+</para></note>
+</refsect2>
+
+<refsect2>
+<title>Shading strategies (similarity to consensus or single sequence)</title>
<para>
Starting with version 3, BOXSHADE has a new shading system. The first
difference is the introduction of a threshold fraction of residues that
@@ -246,7 +329,10 @@
it only influences the shading of the other sequences without being
shown itself.
</para>
-<para>- Consensus display - </para>
+</refsect2>
+
+<refsect2>
+<title>Consensus display</title>
<para>Starting with version 2.5, BOXSHADE
offers the possibility to create an additional line holding a consensus
symbol. This line can either be obtained by using the command line
@@ -277,10 +363,11 @@
LU" where similar residues are represented by lowercase characters and
identical by uppercase characters.
</para>
+</refsect2>
+
+<refsect2>
+<title>Shareware/PD programs useful in conjunction with BOXSHADE</title>
<para>
-- shareware/PD programs useful in conjunction with BOXSHADE -
-</para>
-<para>
multiple alignment files that to be used by BOXSHADE can be created,
amongst others, by the following PD/freeware programs: + PHYLIP by Joe
Felsenstein, available by ftp from anthro.utah.edu + ESEE by Eric Cabot,
@@ -309,10 +396,11 @@
/Fx is to be replaced by the letter of the printer you use. (See the
PRINTGL documentation for further details)
</para>
+</refsect2>
</refsect1>
<refsect1><title>
RESTRICTIONS
-</title></refsect1>
+</title>
<para>
The RTF output and PHYLIP input implementations are still
experimental. Please tell me of your experiences with the program. +
@@ -321,38 +409,30 @@
cannot compile the sources because you are lacking a pascal compiler,
contact the author for precompiled versions
</para>
-<refsect1><title>DISTRIBUTION POLICY</title>
-<para>
-BOXSHADE is completely public-domain and may be passed around and modified without any notice to the author. If you have problems, suggestions or remarks, please contact either of us:
-Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848
-MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany
-E-mail: Kay.Hofmann at memorec.com
-Michael D. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K.
-E-mail: michael.baron at bbsrc.ac.uk
-</para>
</refsect1>
+
<refsect1>
- <title>SEE ALSO</title>
-
- <para>/etc/boxshade/*.par</para>
- <para><application>seaview</application> (1),
- <application>clustalw</application> (1)
+ <title>CITING BOXSHADE</title>
+ <para>
+ There is no publication on BOXSHADE and none is planned. Most people just use it for figures in publications and don't mention anything, this is ok for the authors of BOXSHADE. If you really feel like mentioning BOXSHADE, you could either acknowledge it in the figure legend or in the Mat&Meth part on sequence analysis.
</para>
</refsect1>
+
<refsect1>
- <title>AUTHOR</title>
+ <title>SEE ALSO</title>
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the terms of the &gnu; General Public License, Version 2 any
- later version published by the Free Software Foundation.
+ <para><filename>/etc/boxshade/*.par</filename></para>
+ <para>
+ <citerefentry>
+ <refentrytitle>seaview</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ <citerefentry>
+ <refentrytitle>kalign</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
</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>
- </refsect1>
</refentry>
Modified: trunk/packages/boxshade/trunk/debian/changelog
===================================================================
--- trunk/packages/boxshade/trunk/debian/changelog 2007-02-21 00:08:48 UTC (rev 216)
+++ trunk/packages/boxshade/trunk/debian/changelog 2007-02-24 03:42:36 UTC (rev 217)
@@ -5,12 +5,19 @@
[ Charles Plessy ]
* New version number, but upsteams' 3.3.1 was already packaged in Debian
- under number 3.1.1
+ under number 3.1.1 (Closes: #385255).
* Swiching to collaborative maintainance: Maintainer is a mailing-list,
Uploaders are real people.
- * Using debhelper v5 and conforming to policy 3.7.2.
+ * Tidying the package:
+ - Using debhelper v5 and conforming to policy 3.7.2.
+ - Updated manpage using the template of docbook-xsl 1.71.0.dfsg.1-1.1.
+ - Converted the manpage to unicode.
+ - Added XS-Vcs-Svn and XS-Vcs-Browser to debian/control.
+ - Removed empty files debian/dirs, debian/install, debian/conffiles.
+ * Replaced clustalw (non-freee) by kalign (free) in the Suggests field.
+ * Changed priority to optional.
- -- Steffen Moeller <steffen_moeller at gmx.de> Mon, 8 Jan 2007 15:01:12 +0100
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 24 Feb 2007 11:51:19 +0900
boxshade (3.1.1-1) unstable; urgency=low
Deleted: trunk/packages/boxshade/trunk/debian/conffiles
===================================================================
Modified: trunk/packages/boxshade/trunk/debian/control
===================================================================
--- trunk/packages/boxshade/trunk/debian/control 2007-02-21 00:08:48 UTC (rev 216)
+++ trunk/packages/boxshade/trunk/debian/control 2007-02-24 03:42:36 UTC (rev 217)
@@ -1,15 +1,17 @@
Source: boxshade
Section: science
-Priority: extra
+Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <steffen_moeller at gmx.de>, Charles Plessy <charles-debian-nospam at plessy.org>
Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml
Standards-Version: 3.7.2
+XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/boxshade/trunk/
+XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/boxshade
Package: boxshade
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: seaview, kalign, xfig, clustalw
+Suggests: seaview, kalign, xfig
Description: Pretty-printing of multiple sequence alignments
Boxshade is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does no alignment by
@@ -20,5 +22,5 @@
Various kinds of shading can be applied to identical/similar residues. Output
is written to screen or to a file in the following formats: ANSI/VT100,
PS/EPS, RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT, HTML
-.
+ .
Homepage: http://www.ch.embnet.org/software/BOX_form.html
Modified: trunk/packages/boxshade/trunk/debian/copyright
===================================================================
--- trunk/packages/boxshade/trunk/debian/copyright 2007-02-21 00:08:48 UTC (rev 216)
+++ trunk/packages/boxshade/trunk/debian/copyright 2007-02-24 03:42:36 UTC (rev 217)
@@ -31,4 +31,4 @@
Hartmut: hsc at techfak.uni-kiel.de (don't send Kay or Michael any questions
concerning the 'C' version of boxshade)
-(The comments after the email adresses are form the authors themselves.)
+(The comments after the email addresses are form the authors themselves.)
Deleted: trunk/packages/boxshade/trunk/debian/dirs
===================================================================
Deleted: trunk/packages/boxshade/trunk/debian/install
===================================================================
Modified: trunk/packages/boxshade/trunk/debian/rules
===================================================================
--- trunk/packages/boxshade/trunk/debian/rules 2007-02-21 00:08:48 UTC (rev 216)
+++ trunk/packages/boxshade/trunk/debian/rules 2007-02-24 03:42:36 UTC (rev 217)
@@ -17,14 +17,18 @@
build: build-stamp
-DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
-XP=xsltproc -''-nonet
+XP=xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1"
-boxshade.1: debian/boxshade.xml
- $(XP) $(DB2MAN) $<
+boxshade.1: debian/boxshade.1.xml
+ $(XP) $<
-build-stamp: configure-stamp boxshade.1
+
+build-stamp: boxshade.1
dh_testdir
$(MAKE) -f makefile.unx
touch build-stamp
@@ -32,11 +36,10 @@
clean:
dh_testdir
dh_testroot
- rm -f build-stamp configure-stamp
+ rm -f build-stamp
-$(MAKE) -f makefile.unx clean
+ dh_clean boxshade.1
- dh_clean
-
install: build
dh_testdir
dh_testroot
@@ -66,7 +69,7 @@
# dh_installexamples
# dh_install
dh_installmenu
- dh_installman debian/boxshade.1
+ dh_installman boxshade.1
dh_link
dh_strip
dh_compress
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