[med-svn] r2755 - in trunk/packages/clustalw/trunk: . debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Sun Dec 7 10:59:25 UTC 2008
Author: plessy
Date: 2008-12-07 10:59:25 +0000 (Sun, 07 Dec 2008)
New Revision: 2755
Modified:
trunk/packages/clustalw/trunk/CHANGELOG
trunk/packages/clustalw/trunk/debian/changelog
trunk/packages/clustalw/trunk/debian/clustalw.1
trunk/packages/clustalw/trunk/debian/clustalw.1.xml
trunk/packages/clustalw/trunk/debian/clustalw.install
Log:
Uploaded new upstream version (updated the manpages).
Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG 2008-12-06 23:56:10 UTC (rev 2754)
+++ trunk/packages/clustalw/trunk/CHANGELOG 2008-12-07 10:59:25 UTC (rev 2755)
@@ -1,4 +1,23 @@
----------------------------------------------------------------------
+Version 2.0.10
+----------------------------------------------------------------------
+
+* Fixed g++-4.3 compilation errors
+
+* Added new -quiet command line flag
+
+* Added new -stats=<file> command line flag
+
+* Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms
+
+* Fixed bug 141: profile merging and saving failed
+
+* Fixed bug 139: saving of column quality scores
+
+* Updated help files (new flags, new colour parameter format)
+
+
+----------------------------------------------------------------------
Version 2.0.9
----------------------------------------------------------------------
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-12-06 23:56:10 UTC (rev 2754)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-12-07 10:59:25 UTC (rev 2755)
@@ -1,10 +1,11 @@
-clustalw (2.0.10-1) UNRELEASED; urgency=low
+clustalw (2.0.10-1) unstable; urgency=low
- TODO BEFORE UPLOADING: update the man pages.
-
* New upstream release:
- New -quiet and -stats=<file> command line flags.
- command separator can now be mixed "/" and "-" on all platforms.
+ * debian/clustalw.1*:
+ - added new option and incremented version number.
+ - using Docbook 4.5.
* Added bibliographic information in BibTeX format in debian/reference.
* Using Debhelper 7 (debian/control, debian/compat).
* Enhances: bioperl-run (it has a wrapper for clustalw).
@@ -12,7 +13,7 @@
and is not anymore installed by dh_install (dh_lintian, called by
CDBS, takes care of it).
- -- Charles Plessy <plessy at debian.org> Sat, 15 Nov 2008 18:15:04 +0900
+ -- Charles Plessy <plessy at debian.org> Sun, 07 Dec 2008 19:37:06 +0900
clustalw (2.0.9-1) unstable; urgency=low
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 2008-12-06 23:56:10 UTC (rev 2754)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2008-12-07 10:59:25 UTC (rev 2755)
@@ -1,11 +1,11 @@
.\" Title: CLUSTALW
.\" Author: Des Higgins
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 06/24/2008
+.\" Date: 12/07/2008
.\" Manual: Clustal Manual
-.\" Source: Clustal 2.0.9
+.\" Source: Clustal 2.0.10
.\"
-.TH "CLUSTALW" "1" "06/24/2008" "Clustal 2.0.9" "Clustal Manual"
+.TH "CLUSTALW" "1" "12/07/2008" "Clustal 2.0.10" "Clustal Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -161,7 +161,18 @@
.RS 4
Maximum allowed input sequence length\&.
.RE
+.PP
+\fB\-quiet\fR
+.RS 4
+Reduce console output to minimum\&.
.RE
+.PP
+\fB\-stats=\fR\fB\fIfile\fR\fR
+.RS 4
+Log some alignments statistics to
+\fIfile\fR\&.
+.RE
+.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-12-06 23:56:10 UTC (rev 2754)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-12-07 10:59:25 UTC (rev 2755)
@@ -1,8 +1,8 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
<?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" [
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+ "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
<!-- Template from docbook-xsl-1.73.2.dfsg.1-3 -->
@@ -18,7 +18,7 @@
<!ENTITY dhsurname "Plessy">
<!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "2.0.9">
+ <!ENTITY dhrelease "2.0.10">
<!ENTITY dhtitle "Clustal Manual">
<!ENTITY dhucpackage "CLUSTALW">
<!ENTITY dhpackage "clustalw">
@@ -342,7 +342,7 @@
<para>Sequence range to write starting <replaceable class="parameter">m</replaceable> to <replaceable class="parameter">m</replaceable>+<replaceable class="parameter">n</replaceable>.</para>
</listitem>
</varlistentry>
-
+
<varlistentry>
<term>
<option>-maxseqlen=<replaceable class="parameter">n</replaceable></option>
@@ -351,6 +351,24 @@
<para>Maximum allowed input sequence length.</para>
</listitem>
</varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-quiet</option>
+ </term>
+ <listitem>
+ <para>Reduce console output to minimum.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-stats=<replaceable class="parameter">file</replaceable></option>
+ </term>
+ <listitem>
+ <para>Log some alignments statistics to <replaceable class="parameter">file</replaceable>.</para>
+ </listitem>
+ </varlistentry>
</variablelist>
</refsect3>
Modified: trunk/packages/clustalw/trunk/debian/clustalw.install
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.install 2008-12-06 23:56:10 UTC (rev 2754)
+++ trunk/packages/clustalw/trunk/debian/clustalw.install 2008-12-07 10:59:25 UTC (rev 2755)
@@ -1,2 +1 @@
clustalw_help usr/share/clustalw
-debian/overrides/clustalw usr/share/lintian/overrides
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