[med-svn] r1816 - trunk/packages/dialign-t/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Wed Apr 30 01:01:26 UTC 2008
Author: plessy
Date: 2008-04-30 01:01:26 +0000 (Wed, 30 Apr 2008)
New Revision: 1816
Modified:
trunk/packages/dialign-t/trunk/debian/README.Debian
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/control
trunk/packages/dialign-t/trunk/debian/copyright
trunk/packages/dialign-t/trunk/debian/dialign-tx.1
trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml
trunk/packages/dialign-t/trunk/debian/rules
Log:
Working towards update.
Modified: trunk/packages/dialign-t/trunk/debian/README.Debian
===================================================================
--- trunk/packages/dialign-t/trunk/debian/README.Debian 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/README.Debian 2008-04-30 01:01:26 UTC (rev 1816)
@@ -1,24 +1,13 @@
-dialign-t for Debian
+DIALIGN-TX for Debian
--------------------
The configuration directory shipped with the source is installed in
-/usr/share/dialign-t on your system.
+/usr/share/dialign-tx on your system.
Possible issues with this package:
- - dialign-t is compiled with the -Os optimisation level, while in the upstream
- sources -O3 is used. The reason is gcc-4.2, the current default compiler,
- can not build dialign-t with -01,2 or 3. A benchmark made by aligning 43
- bHLH proteins suggests that the impact on the speed is not worse than 10 %.
-
- - Users have no write acces to /usr/share/dialign-t, so problems are expected
+ - Users have no write acces to /usr/share/dialign-tx, so problems are expected
when running dialign-t -C.
- - I had to remove the documentation because I did not manage to contact its
- author to get its LaTeX sources. I apologise for doing this. In the
- meantime, very similar informations can be found in the manpage I wrote for
- dialign-t. TO BE COMPLIANT WITH THE DEBIAN FREE SOFTWARE GUIDELINES, THE
- DOCUMENTATION IS ALSO REMOVED FROM THE ORIGINAL SOURCES.
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 9 Oct 2007 23:17:04 +0900
+ -- Charles Plessy <plessy at debian.org> Fri, 04 Apr 2008 11:23:25 +0900
Modified: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2008-04-30 01:01:26 UTC (rev 1816)
@@ -9,9 +9,9 @@
* debian/copyright:
- Converted to machine-readable format.
- Updated relevant copyrights for 2008.
- * Updated my email address.
+ * Updated my email address.
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:01:46 +0900
+ -- Charles Plessy <plessy at debian.org> Sat, 22 Mar 2008 11:46:01 +0900
dialign-t (0.2.2.dfsg-1) unstable; urgency=low
Modified: trunk/packages/dialign-t/trunk/debian/control
===================================================================
--- trunk/packages/dialign-t/trunk/debian/control 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/control 2008-04-30 01:01:26 UTC (rev 1816)
@@ -4,7 +4,7 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 5)
+Build-Depends: debhelper (>= 5), cdbs
Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dialign-t/trunk/
@@ -12,7 +12,10 @@
Package: dialign-tx
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-t-data (= ${source:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends}, dialign-tx-data (= ${source:Version})
+Conflicts: dialign-t, dialign-t-doc
+Replaces: dialign-t, dialign-t-doc
+Provides: dialign-t, dialign-t-doc
Enhances: t-coffee
Description: Segment-based multiple sequence alignment
DIALIGN-TX is a command line tool to perform multiple alignment of protein or
@@ -20,7 +23,6 @@
including several new improvements and heuristics that significantly enhance
the quality of the output alignments compared to DIALIGN 2.2. For pairwise
alignment, DIALIGN-TX
-CHECK
uses a fragment-chaining algorithm that favours chains of
low-scoring local alignments over isolated high-scoring fragments. For
multiple alignment, DIALIGN-T uses an improved greedy procedure that is less
@@ -34,13 +36,12 @@
DIALIGN-T has been published in Amarendran R. Subramanian, Jan Weyer-Menkhoff,
Michael Kaufmann, Burkhard Morgenstern: DIALIGN-T: An improved algorithm for
segment-based multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
-UPDATE
Package: dialign-tx-data
Architecture: all
Depends: ${misc:Depends}
-Recommends: dialign-t (= ${source:Version})
+Recommends: dialign-t (= ${binary:Version})
Description: Common data files for dialign-t
This package contain the score matrices and probability distribution files
that DIALIGN-TX needs to align peptidic and nucleic sequences.
Modified: trunk/packages/dialign-t/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign-t/trunk/debian/copyright 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/copyright 2008-04-30 01:01:26 UTC (rev 1816)
@@ -1,5 +1,5 @@
X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
+X-Debianized-By: Charles Plessy <plessy at debian.org>
X-Debianized-Date: Tue, 9 Oct 2007 23:17:04 +0900
X-Source-Downloaded-From: http://dialign-tx.gobics.de
X-Upstream-Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
@@ -7,7 +7,7 @@
Files: debian/*
-Copyright: © 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+Copyright: © 2007-2008 Charles Plessy <plessy at debian.org>
© 2008 David Paleino <d.paleino at gmail.com>
License: LGPL-2.1+
Modified: trunk/packages/dialign-t/trunk/debian/dialign-tx.1
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1 2008-04-30 01:01:26 UTC (rev 1816)
@@ -1,23 +1,23 @@
-.\" Title: DIALIGN-T
+.\" Title: DIALIGN-TX
.\" Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 11/14/2007
-.\" Manual: DiAlign-T: Parameters
-.\" Source: dialign-t 0.2.2
+.\" Date: 04/30/2008
+.\" Manual: DiAlign-TX: Parameters
+.\" Source: dialign-tx 1.0.0
.\"
-.TH "DIALIGN\-T" "1" "11/14/2007" "dialign-t 0.2.2" "DiAlign-T: Parameters"
+.TH "DIALIGN\-TX" "1" "04/30/2008" "dialign-tx 1.0.0" "DiAlign-TX: Parameters"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dialign-t - Segment-based multiple sequence alignment
+dialign-tx - Segment-based multiple sequence alignment
.SH "SYNOPSIS"
-.HP 10
-\fBdialign\-t\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
+.HP 11
+\fBdialign\-tx\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
.SH "DESCRIPTION"
.PP
-DIALIGN\-T is an improved algorithm for segment\-based multiple protein alignments\. DIALIGN\-T is a complete reimplementation of the segment\-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2\.2\. This significant superiority has been observed on local as well on global alignment benchmarks\.
+DIALIGN\-TX is an improved algorithm for segment\-based multiple protein alignments\. DIALIGN\-TX is a complete reimplementation of the segment\-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2\.2\. This significant superiority has been observed on local as well on global alignment benchmarks\.
.SH "OPTIONS"
.PP
\fB\-d\fR
@@ -48,6 +48,17 @@
Maximum amount of characters per line when printing a sequence [DEFAULT 80]\.
.RE
.PP
+\fB\-l\fR
+.RS 4
+sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0]
+.IP "" 4
+0 switched off
+.IP "" 4
+1 level\-1, reduced sensitivity
+.IP "" 4
+2 level\-2, strongly reduced sensitivity
+.RE
+.PP
\fB\-m\fR
.RS 4
Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\.scr] / [DEFAULT DNA: dna_matrix\.scr]\.
@@ -173,9 +184,14 @@
Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output]\.
.RE
.PP
+\fB\-F\fR
+.RS 4
+Fast mode (implies \-l0, since it already significantly reduces sensitivity)\.
+.RE
+.PP
\fB\-C\fR
.RS 4
-Generate probability table saved in /usr/share/dialign\-t/prob_table and exit\.
+Generate probability table saved in /usr/share/dialign\-tx/prob_table and exit\.
.RE
.PP
\fB\-H\fR, \fB\-h\fR
@@ -184,60 +200,62 @@
.RE
.SH "FILES"
.PP
-\fI/usr/share/dialign\-t\fR
+\fI/usr/share/dialign\-tx\fR
.RS 4
This is the default conf\-directory that
-\fBdialign\-t\fR
+\fBdialign\-tx\fR
expects as its first argument, as supplied in the upstream sources\.
.RE
.SH "SEE ALSO"
.PP
-DIALIGN\-T is a re\-implementation of
+DIALIGN\-TX is a re\-implementation of
\fBdialign2-2\fR(1)\. (See http://dialign\.gobics\.de/ for more information about DIALIGN2)\.
.PP
-The website of DIALIGN\-T is http://dialign\-t\.gobics\.de/
-.SH "REFERENCE"
+The website of DIALIGN\-TX is http://dialign\-tx\.gobics\.de/
+.SH "REFERENCES"
.PP
-Amarendran R\. Subramanian, Jan Weyer\-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-T: An improved algorithm for segment\-based multiple sequence alignment BMC Bioinformatics 2005, 6:66\.
+Amarendran R\. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-TX: improvement of the segment\-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies\. In Progress, 2008\.
+.PP
+Amarendran R\. Subramanian, Jan Weyer\-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-T: An improved algorithm for segment\-based multiple sequence alignment\. BMC Bioinformatics 2005, 6:66\.
.SH "AUTHORS"
.PP
\fBAmarendran R\. Subramanian\fR <\&subraman at informatik\.uni\-tuebingen\.de\&>
.sp -1n
.IP "" 4
-Author of dialign\-t
+Author of dialign\-tx
.PP
\fBVolker Menrad\fR
.sp -1n
.IP "" 4
-Co\-author of dialign\-t
+Co\-author of dialign\-tx
.PP
\fBDorothea Emig\fR
.sp -1n
.IP "" 4
-Co\-author of dialign\-t
+Co\-author of dialign\-tx
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\.org\&>
.sp -1n
.IP "" 4
Converted this guide in DocBook XML for the Debian distribution\.
.SH "COPYRIGHT"
-Copyright \(co 2004, 2005, 2006, 2007 Amarendran R. Subramanian
+Copyright \(co 2004, 2005, 2006, 2007 Amarendran R. Subramanian (DiAlign-TX)
.br
-Copyright \(co 2004 Volker Menrad
+Copyright \(co 2004 Volker Menrad (DiAlign-TX)
.br
-Copyright \(co 2004 Dorothea Emig
+Copyright \(co 2004 Dorothea Emig (DiAlign-TX)
.br
-Copyright \(co 2007 Charles Plessy
+Copyright \(co 2007 Charles Plessy (This document and its XML source.)
.br
.PP
-DiAlign\-T is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2\.1 of the License, or (at your option) any later version\.
+DiAlign\-TX is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2\.1 of the License, or (at your option) any later version\.
.PP
-DiAlign\-T is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE\. See the GNU Lesser General Public License for more details\.
+DiAlign\-TX is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE\. See the GNU Lesser General Public License for more details\.
.PP
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc\., 51 Franklin St, Fifth Floor, Boston, MA 02110\-1301 USA
.PP
On Debian system, a copy of the GNU Lesser General Public License is available in
\fI/usr/share/common\-licences\fR\.
.PP
-This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign\-T itself\.
+This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign\-TX itself\.
.sp
Modified: trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml 2008-04-30 01:01:26 UTC (rev 1816)
@@ -16,7 +16,7 @@
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1.0.0">
<!ENTITY dhtitle "DiAlign-TX: Parameters">
@@ -25,7 +25,7 @@
<!ENTITY dhproduct "&dhpackage;">
<!ENTITY dhsection "1">
- <!ENTITY config-dir "/usr/share/dialign-t">
+ <!ENTITY config-dir "/usr/share/dialign-tx">
]>
<refentry>
@@ -72,30 +72,30 @@
<year>2005</year>
<year>2006</year>
<year>2007</year>
- <holder> Amarendran R. Subramanian</holder>
+ <holder>Amarendran R. Subramanian (DiAlign-TX)</holder>
</copyright>
<copyright>
<year>2004</year>
- <holder>Volker Menrad</holder>
+ <holder>Volker Menrad (DiAlign-TX)</holder>
</copyright>
<copyright>
<year>2004</year>
- <holder>Dorothea Emig</holder>
+ <holder>Dorothea Emig (DiAlign-TX)</holder>
</copyright>
<copyright>
<year>2007</year>
- <holder>&dhusername;</holder>
+ <holder>&dhusername; (This document and its XML source.)</holder>
</copyright>
<legalnotice>
<para>
- DiAlign-T is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
+ DiAlign-TX is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
</para>
<para>
- DiAlign-T is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+ DiAlign-TX is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
</para>
<para>
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
@@ -104,7 +104,7 @@
On Debian system, a copy of the GNU Lesser General Public License is available in <filename class="directory">/usr/share/common-licences</filename>.
</para>
<para>
- This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign-T itself.
+ This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign-TX itself.
</para>
</legalnotice>
</refentryinfo>
@@ -131,7 +131,7 @@
<refsect1 id="description">
<title>DESCRIPTION</title>
<para>
- DIALIGN-T is an improved algorithm for segment-based multiple protein alignments. DIALIGN-T is a complete reimplementation of the segment-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2. This significant superiority has been observed on local as well on global alignment benchmarks.
+ DIALIGN-TX is an improved algorithm for segment-based multiple protein alignments. DIALIGN-TX is a complete reimplementation of the segment-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2.2. This significant superiority has been observed on local as well on global alignment benchmarks.
</para>
</refsect1>
@@ -178,6 +178,20 @@
</varlistentry>
<varlistentry>
+ <term><option>-l</option></term>
+ <listitem>
+ <para>
+ sensitivity mode, the higher the level the less likely spurious random fragments are aligned in local alignments [DEFAULT 0]
+ <simplelist>
+ <member>0 switched off</member>
+ <member>1 level-1, reduced sensitivity</member>
+ <member>2 level-2, strongly reduced sensitivity</member>
+ </simplelist>
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
<term><option>-m</option></term>
<listitem>
<para>
@@ -327,8 +341,17 @@
</para>
</listitem>
</varlistentry>
-
+
<varlistentry>
+ <term><option>-F</option></term>
+ <listitem>
+ <para>
+ Fast mode (implies -l0, since it already significantly reduces sensitivity).
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
<term><option>-C</option></term>
<listitem>
<para>
@@ -364,15 +387,18 @@
<refsect1 id="see_also">
<title>SEE ALSO</title>
- <para>DIALIGN-T is a re-implementation of <citerefentry><refentrytitle>dialign2-2</refentrytitle><manvolnum>1</manvolnum></citerefentry>. (See http://dialign.gobics.de/ for more information about DIALIGN2).
+ <para>DIALIGN-TX is a re-implementation of <citerefentry><refentrytitle>dialign2-2</refentrytitle><manvolnum>1</manvolnum></citerefentry>. (See http://dialign.gobics.de/ for more information about DIALIGN2).
</para>
- <para>The website of DIALIGN-T is http://dialign-t.gobics.de/</para>
+ <para>The website of DIALIGN-TX is http://dialign-tx.gobics.de/</para>
</refsect1>
<refsect1 id="reference">
- <title>REFERENCE</title>
- <para>Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern:
- DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
- BMC Bioinformatics 2005, 6:66.</para>
+ <title>REFERENCES</title>
+ <para>
+ Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies. In Progress, 2008.
+ </para>
+ <para>
+ Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
+ </para>
</refsect1>
</refentry>
Modified: trunk/packages/dialign-t/trunk/debian/rules
===================================================================
--- trunk/packages/dialign-t/trunk/debian/rules 2008-04-30 00:13:49 UTC (rev 1815)
+++ trunk/packages/dialign-t/trunk/debian/rules 2008-04-30 01:01:26 UTC (rev 1816)
@@ -1,52 +1,9 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-CFLAGS = -Wall -g
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2 Please revert to O2 when bug 446714 is fixed
-endif
+DEB_SRCDIR = $(CURDIR)/source
-build: build-stamp
-build-stamp:
- dh_testdir
- $(MAKE) --directory=source CPPFLAGS='' CFLAGS='$(CFLAGS)'
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp
- $(MAKE) -C source clean
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
- dh_install
+binary-fixup/dialign-tx-data::
chmod 644 $(CURDIR)/debian/dialign-tx-data/usr/share/dialign-tx/*
-
-binary-indep: build install
-
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installman debian/dialign-t.1
- dh_installdocs
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
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