[med-svn] r229 - trunk/packages/amap-align/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Mar 10 07:42:26 CET 2007
Author: charles-guest
Date: 2007-03-10 06:42:25 +0000 (Sat, 10 Mar 2007)
New Revision: 229
Modified:
trunk/packages/amap-align/trunk/debian/amap.1.xml
trunk/packages/amap-align/trunk/debian/changelog
trunk/packages/amap-align/trunk/debian/rules
Log:
Manpage and building improvements
Modified: trunk/packages/amap-align/trunk/debian/amap.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1.xml 2007-03-10 05:36:47 UTC (rev 228)
+++ trunk/packages/amap-align/trunk/debian/amap.1.xml 2007-03-10 06:42:25 UTC (rev 229)
@@ -1,34 +1,60 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
+<?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" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy>">
+ <!ENTITY dhdate "March 10, 2007">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhucpackage "<refentrytitle>AMAP</refentrytitle>">
<!ENTITY dhpackage "amap-align">
+ <!ENTITY dhrelease "2.0">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+ <!ENTITY dhtitle "User Manual">
]>
+<!-- This manpage is inspired from the template of docbook-xsl 1.71.0.dfsg.1-1.1 -->
+
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
- <copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Ariel</firstname>
+ <surname>Schwartz</surname>
+ <contrib>Upstream author of AMAP</contrib>
+ <address>
+ <email>sariel at cs.berkeley.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote Probcons, on which AMAP is based.</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>
+ AMAP, PROBCONS, and this manual page have been made freely available as PUBLIC DOMAIN software and hence are not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. AMAP, PROBCONS and this manual page are distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program.
+ </para>
+ </legalnotice>
</refentryinfo>
<refmeta>
&dhucpackage;
@@ -238,7 +264,12 @@
<refsect1>
<title>SEE ALSO</title>
- <para>The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README in <filename>/usr/share/doc/amap-align/</filename>). Future releases might implement the algorithm using a new independent code base. On &debian; systems, PROBCONS is available in the probcons package.</para>
+ <para>
+ The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README in <filename>/usr/share/doc/amap-align/</filename>). Future releases might implement the algorithm using a new independent code base.
+ </para>
+
+ <para>
+ On &debian; systems, <citerefentry><refentrytitle>probcons</refentrytitle><manvolnum>1</manvolnum></citerefentry> is available in the probcons package.</para>
</refsect1>
<refsect1>
@@ -251,23 +282,5 @@
PROBCONS was published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.
</para>
</refsect1>
-
- <refsect1>
- <title>AUTHORS</title>
- <itemizedlist>
- <listitem><para>PROBCONS was written by Chuong Do.</para></listitem>
- <listitem><para>AMAP algorithm implemented by Ariel Schwartz (<email>sariel at cs.berkeley.edu</email>).</para></listitem>
- <listitem><para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).</para></listitem>
- </itemizedlist>
- </refsect1>
- <refsect1>
- <title>LICENCE</title>
- <para>
- AMAP comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. See the files README and README.PROBCONS for details.
- </para>
- <para>This manpage is hereby placed in the public domain.</para>
- </refsect1>
-
-
</refentry>
Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog 2007-03-10 05:36:47 UTC (rev 228)
+++ trunk/packages/amap-align/trunk/debian/changelog 2007-03-10 06:42:25 UTC (rev 229)
@@ -3,9 +3,11 @@
* Add Subversion repository URL to debian/control.
* Patching for building with gcc-4.3. Many thanks to Martin Michlmayr (Closes:413477)
* Renaming /usr/bin/amap-align to /usr/bin/amap
- * Including /usr/share/dpatch/dpatch.make in debian/rules.
+ * Including /usr/share/dpatch/dpatch.make in debian/rules.
+ * Improving manpage using the template of docbook-xsl 1.71.0.dfsg.1-1.1.
+ * Fixing double-building in debian/rules.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 14:26:13 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 15:41:10 +0900
amap-align (2.0-1) unstable; urgency=low
Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules 2007-03-10 05:36:47 UTC (rev 228)
+++ trunk/packages/amap-align/trunk/debian/rules 2007-03-10 06:42:25 UTC (rev 229)
@@ -9,8 +9,13 @@
# be used without restriction.
DB2MAN = "/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl"
-XP = xsltproc -o debian/ -''-nonet
+XP=xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1"
+
CFLAGS = -Wall -g
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
@@ -21,18 +26,23 @@
include /usr/share/dpatch/dpatch.make
-build: patch
+build: build-stamp
+
+build-stamp: patch amap.1
dh_testdir
- $(XP) $(DB2MAN) debian/amap.1.xml
$(MAKE)
touch build-stamp
+amap.1: debian/amap.1.xml
+ $(XP) $<
+
+
clean: unpatch
dh_testdir
dh_testroot
rm -f build-stamp
-$(MAKE) clean
- dh_clean debian/amap.1
+ dh_clean amap.1
install: build
dh_testdir
@@ -49,7 +59,7 @@
dh_installdocs
dh_installexamples
dh_install amap usr/bin/
- dh_installman debian/amap.1
+ dh_installman amap.1
dh_link usr/bin/amap usr/bin/amap-align \
usr/share/man/man1/amap.1 usr/share/man/man1/amap-align.1
dh_strip
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