[med-svn] r690 - in trunk/packages/dialign-t/trunk: . debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Oct 13 09:16:47 UTC 2007
Author: charles-guest
Date: 2007-10-13 09:16:47 +0000 (Sat, 13 Oct 2007)
New Revision: 690
Added:
trunk/packages/dialign-t/trunk/debian/
trunk/packages/dialign-t/trunk/debian/README.Debian
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/compat
trunk/packages/dialign-t/trunk/debian/control
trunk/packages/dialign-t/trunk/debian/copyright
trunk/packages/dialign-t/trunk/debian/dialign-t.1
trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml
trunk/packages/dialign-t/trunk/debian/dialign-t.doc-base
trunk/packages/dialign-t/trunk/debian/install
trunk/packages/dialign-t/trunk/debian/rules
trunk/packages/dialign-t/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/dialign-t/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/dialign-t/trunk/debian/README.Debian
===================================================================
--- trunk/packages/dialign-t/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/README.Debian 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,17 @@
+dialign-t for Debian
+--------------------
+
+The configuration directory shipped with the source is installed in
+/usr/share/dialign-t on your system.
+
+
+Possible issues with this package:
+
+ - dialign-t is compiled with the -O2 optimisation level, while in the upstream
+ sources -O3 is used. I will perform benchmarks later to see what is the most
+ appropriate.
+
+ - Users have no write acces to /usr/share/dialign-t, so problems are expected
+ when running dialign-t -C.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 9 Oct 2007 23:17:04 +0900
Added: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,6 @@
+dialign-t (0.2.2-1) unstable; urgency=low
+
+ * Initial release (Closes: #445983)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 9 Oct 2007 23:17:04 +0900
+
Added: trunk/packages/dialign-t/trunk/debian/compat
===================================================================
--- trunk/packages/dialign-t/trunk/debian/compat (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/compat 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1 @@
+5
Added: trunk/packages/dialign-t/trunk/debian/control
===================================================================
--- trunk/packages/dialign-t/trunk/debian/control (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/control 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,27 @@
+Source: dialign-t
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), quilt
+Standards-Version: 3.7.2
+XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/dialign-t/trunk/
+XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dialign-t
+Homepage: http://dialign-t.gobics.de/
+
+Package: dialign-t
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Segment-based multiple sequence alignment
+ DIALIGN-T is a command line tool to perform multiple alignment of protein or
+ DNA sequences. It 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. For pairwise
+ alignment, DIALIGN-T 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
+ sensitive to spurious local sequence similarities.
+ .
+ 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.
Added: trunk/packages/dialign-t/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign-t/trunk/debian/copyright (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/copyright 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,38 @@
+This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
+Tue, 9 Oct 2007 23:17:04 +0900.
+
+It was downloaded from <http://dialign-t.gobics.de/>
+
+Upstream Authors:
+
+ Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+ Volker Menrad
+ Dorothea Emig
+
+Copyright:
+
+ Copyright 2004-2007 Amarendran R. Subramanian
+ Copyright 2004 Volker Menrad
+ Copyright 2004 Dorothea Emig
+
+License:
+
+ This package 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.
+
+ This package 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.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU Lesser General
+Public License can be found in `/usr/share/common-licenses/LGPL'.
+
+The Debian packaging is © 2007, Charles Plessy and is licensed under the same
+terms as DIALIGN-T itself.
Added: trunk/packages/dialign-t/trunk/debian/dialign-t.1
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.1 (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.1 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,238 @@
+.\" Title: DIALIGN-T
+.\" Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+.\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
+.\" Date: 10/13/2007
+.\" Manual: DiAlign-T: Parameters
+.\" Source: dialign-t 0.2.2
+.\"
+.TH "DIALIGN\-T" "1" "10/13/2007" "dialign\-t 0.2.2" "DiAlign\-T: Parameters"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+dialign\-t \- Segment\-based multiple sequence alignment
+.SH "SYNOPSIS"
+.HP 10
+\fBdialign\-t\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.
+.SH "OPTIONS"
+.PP
+\fB\-d\fR
+.RS 4
+Debug\-Mode [DEFAULT 0]
+.IP "" 4
+0 no debug statements
+.IP "" 4
+1 debugs the current phase of the processing
+.IP "" 4
+2 very loquacious debugging
+.IP "" 4
+5 hardcore debugging
+.RE
+.PP
+\fB\-s\fR
+.RS 4
+Maximum amount of input sequences [DEFAULT 5000].
+.RE
+.PP
+\fB\-a\fR
+.RS 4
+Maximum number of characters per line in a FASTA file [DEFAULT 100].
+.RE
+.PP
+\fB\-c\fR
+.RS 4
+Maximum amount of characters per line when printing a sequence [DEFAULT 80].
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.scr] / [DEFAULT DNA: dna_matrix.scr].
+.RE
+.PP
+\fB\-w\fR
+.RS 4
+Defines the minimum weight when the weight formula is changed to 1\-pow(1\-prob, factor) [DEFAULT 0.000000065].
+.RE
+.PP
+\fB\-p\fR
+.RS 4
+Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000].
+.RE
+.PP
+\fB\-v\fR
+.RS 4
+Add to each score (to prevent negative values) [DEFAULT 0].
+.RE
+.PP
+\fB\-t\fR
+.RS 4
+
+\(lqEven\(rq
+threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0].
+.RE
+.PP
+\fB\-n\fR
+.RS 4
+Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1].
+.RE
+.PP
+\fB\-g\fR
+.RS 4
+Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1].
+.RE
+.PP
+\fB\-m\fR
+.RS 4
+Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4.0] / [DEFAULT DNA: 0.9].
+.RE
+.PP
+\fB\-o\fR
+.RS 4
+Wether overlap weights are calculated or not [DEFAULT 0].
+.RE
+.PP
+\fB\-f\fR
+.RS 4
+Minimum fragment length [DEFAULT 1].
+.RE
+.PP
+\fB\-r\fR
+.RS 4
+Threshold weight to consider the fragment at all [DEFAULT 0.0].
+.RE
+.PP
+\fB\-u\fR
+.RS 4
+[DEFAULT 0]
+.IP "" 4
+
+ 1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance).
+
+.IP "" 4
+
+ 0: All pairwise alignments will be calculated.
+
+.RE
+.PP
+\fB\-D\fR
+.RS 4
+Input is DNA\-sequence.
+.RE
+.PP
+\fB\-T\fR
+.RS 4
+Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0).
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+\fBWarning\fR
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded).
+
+.RE
+.PP
+\fB\-L\fR
+.RS 4
+Compare only longest Open Reading Frame.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+\fBWarning\fR
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded).
+
+.RE
+.PP
+\fB\-O\fR
+.RS 4
+Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+\fBWarning\fR
+Do not use
+\fB\-D\fR
+with this option (Default values for PROTEIN input will be loaded).
+
+.RE
+.PP
+\fB\-P\fR
+.RS 4
+Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output].
+.RE
+.PP
+\fB\-C\fR
+.RS 4
+Generate probability table saved in /usr/share/dialign\-t/prob_table and exit.
+.RE
+.PP
+\fB\-H\fR, \fB\-h\fR
+.RS 4
+Print this message.
+.RE
+.SH "FILES"
+.PP
+\fI/usr/share/dialign\-t\fR
+.RS 4
+This is the defauld conf\-directory that
+\fBdialign\-t\fR
+expects as its first argument, as supplied in the upstream sources.
+.RE
+.SH "SEE ALSO"
+.PP
+
+\fBdialign2\-2\fR(1)
+.SH "AUTHORS"
+.PP
+\fBAmarendran R. Subramanian\fR <\&subraman at informatik.uni\-tuebingen.de\&>
+.sp -1n
+.IP "" 4
+Author of dialign\-t
+.PP
+\fBVolker Menrad\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-t
+.PP
+\fBDorothea Emig\fR
+.sp -1n
+.IP "" 4
+Co\-author of dialign\-t
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy.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
+.br
+Copyright \(co 2004 Volker Menrad
+.br
+Copyright \(co 2004 Dorothea Emig
+.br
+Copyright \(co 2007 Charles Plessy
+.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.
+.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.
+.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.
+.br
Added: trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.1.xml 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,376 @@
+<?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" [
+
+<!-- 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' -->
+
+<!-- Template from docbook-xsl 1.73.2.dfsg.1-2 -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "0.2.2">
+ <!ENTITY dhtitle "DiAlign-T: Parameters">
+ <!ENTITY dhucpackage "DIALIGN-T">
+ <!ENTITY dhpackage "dialign-t">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhsection "1">
+
+ <!ENTITY config-dir "/usr/share/dialign-t">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Amarendran R.</firstname>
+ <surname>Subramanian</surname>
+ <contrib>Author of &dhpackage;</contrib>
+ <address>
+ <email>subraman at informatik.uni-tuebingen.de</email>
+ </address>
+ </author>
+
+ <author>
+ <firstname>Volker</firstname>
+ <surname>Menrad</surname>
+ <contrib>Co-author of &dhpackage;</contrib>
+ </author>
+
+ <author>
+ <firstname>Dorothea</firstname>
+ <surname>Emig</surname>
+ <contrib>Co-author of &dhpackage;</contrib>
+ </author>
+ </authorgroup>
+
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Converted this guide in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+
+ <copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder> Amarendran R. Subramanian</holder>
+ </copyright>
+
+ <copyright>
+ <year>2004</year>
+ <holder>Volker Menrad</holder>
+ </copyright>
+
+ <copyright>
+ <year>2004</year>
+ <holder>Dorothea Emig</holder>
+ </copyright>
+
+ <copyright>
+ <year>2007</year>
+ <holder>&dhusername;</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.
+ </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.
+ </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
+ </para>
+ <para>
+ 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.
+ </para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Segment-based multiple sequence alignment</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>OPTIONS</option></arg>
+ <arg choice="req"><replaceable>conf-directory</replaceable></arg>
+ <arg choice="req"><replaceable>fasta-file</replaceable></arg>
+ <arg choice="opt"><replaceable>fasta-out-file</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <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.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+
+ <varlistentry>
+ <term><option>-d</option></term>
+ <listitem>
+ <para>Debug-Mode [DEFAULT 0]</para>
+ <simplelist>
+ <member>0 no debug statements</member>
+ <member>1 debugs the current phase of the processing</member>
+ <member>2 very loquacious debugging</member>
+ <member>5 hardcore debugging</member>
+ </simplelist>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-s</option></term>
+ <listitem>
+ <para>Maximum amount of input sequences [DEFAULT 5000].</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-a</option></term>
+ <listitem>
+ <para>Maximum number of characters per line in a FASTA file [DEFAULT 100].</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-c</option></term>
+ <listitem>
+ <para>Maximum amount of characters per line when printing a sequence
+ [DEFAULT 80].</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-m</option></term>
+ <listitem>
+ <para>
+ Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.scr] / [DEFAULT DNA: dna_matrix.scr].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-w</option></term>
+ <listitem>
+ <para>
+ Defines the minimum weight when the weight formula is changed to 1-pow(1-prob, factor) [DEFAULT 0.000000065].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-p</option></term>
+ <listitem>
+ <para>
+ Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000].
+ </para>
+ </listitem>
+ </varlistentry>
+
+
+ <varlistentry>
+ <term><option>-v</option></term>
+ <listitem>
+ <para>
+ Add to each score (to prevent negative values) [DEFAULT 0].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-t</option></term>
+ <listitem>
+ <para>
+ <quote>Even</quote> threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-n</option></term>
+ <listitem>
+ <para>
+ Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-g</option></term>
+ <listitem>
+ <para>Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-m</option></term>
+ <listitem>
+ <para>
+ Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4.0] / [DEFAULT DNA: 0.9].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-o</option></term>
+ <listitem>
+ <para>Wether overlap weights are calculated or not [DEFAULT 0].</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-f</option></term>
+ <listitem>
+ <para>Minimum fragment length [DEFAULT 1].</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-r</option></term>
+ <listitem>
+ <para>Threshold weight to consider the fragment at all [DEFAULT 0.0]. </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-u</option></term>
+ <listitem>
+ <para>[DEFAULT 0]</para>
+ <simplelist>
+ <member>
+ 1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance).
+ </member>
+ <member>
+ 0: All pairwise alignments will be calculated.
+ </member>
+ </simplelist>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-D</option></term>
+ <listitem>
+ <para>Input is DNA-sequence.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-T</option></term>
+ <listitem>
+ <para>
+ Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0). <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-L</option></term>
+ <listitem>
+ <para>
+ Compare only longest Open Reading Frame. <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-O</option></term>
+ <listitem>
+ <para>
+ Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF. <warning><para>Do not use <option>-D</option> with this option (Default values for PROTEIN input will be loaded).</para></warning>
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-P</option></term>
+ <listitem>
+ <para>
+ Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output].
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-C</option></term>
+ <listitem>
+ <para>
+ Generate probability table saved in &config-dir;/prob_table and exit.
+ </para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-H</option></term>
+ <term><option>-h</option></term>
+ <listitem>
+ <para> Print this message.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="files">
+ <title>FILES</title>
+ <variablelist>
+ <varlistentry>
+ <term><filename>&config-dir;</filename></term>
+ <listitem>
+ <para>
+ This is the defauld conf-directory that <command>&dhpackage;</command> expects as its first argument, as supplied in the upstream sources.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para>
+ <citerefentry>
+ <refentrytitle>dialign2-2</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>
+ </para>
+ </refsect1>
+</refentry>
+
Added: trunk/packages/dialign-t/trunk/debian/dialign-t.doc-base
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-t.doc-base (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/dialign-t.doc-base 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,14 @@
+Document: dialign-t
+Title: DiAlign-T: Parameters
+Author: Volker Menrad
+Section: Applications/Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/dialign-t/user_guide.pdf
+
+Format: postscript
+Files: /usr/share/doc/dialign-t/user_guide.ps
+
+Format: HTML
+Index: /usr/share/doc/dialign-t/html/index.html
+Files: /usr/share/doc/dialign-t/html/*.html
Added: trunk/packages/dialign-t/trunk/debian/install
===================================================================
--- trunk/packages/dialign-t/trunk/debian/install (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/install 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,2 @@
+conf/* usr/share/dialign-t/
+source/dialign-t usr/bin
Added: trunk/packages/dialign-t/trunk/debian/rules
===================================================================
--- trunk/packages/dialign-t/trunk/debian/rules (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/rules 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,55 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+include /usr/share/quilt/quilt.make
+
+build: patch build-stamp
+build-stamp:
+ dh_testdir
+ $(MAKE) --directory=source CPPFLAGS='' CFLAGS='$(CFLAGS)'
+ touch $@
+
+clean: unpatch
+ 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
+ chmod 644 $(CURDIR)/debian/dialign-t/usr/share/dialign-t/*
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs doc/html doc/user_guide.pdf doc/user_guide.ps
+ dh_installexamples
+ dh_installman debian/dialign-t.1
+ dh_link
+ dh_strip
+ dh_compress -Xpdf -Xps
+ 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
Property changes on: trunk/packages/dialign-t/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/dialign-t/trunk/debian/watch
===================================================================
--- trunk/packages/dialign-t/trunk/debian/watch (rev 0)
+++ trunk/packages/dialign-t/trunk/debian/watch 2007-10-13 09:16:47 UTC (rev 690)
@@ -0,0 +1,3 @@
+version=3
+
+http://dialign-t.gobics.de/ DIALIGN-T_(.*)\.tar\.gz
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