[med-svn] r19 - in trunk/packages/dialign/trunk: . debian
debian/patches
Charles Plessy
charles-guest at costa.debian.org
Tue Apr 18 12:58:16 UTC 2006
Author: charles-guest
Date: 2006-04-18 12:58:15 +0000 (Tue, 18 Apr 2006)
New Revision: 19
Added:
trunk/packages/dialign/trunk/debian/
trunk/packages/dialign/trunk/debian/BUGS
trunk/packages/dialign/trunk/debian/README.Debian
trunk/packages/dialign/trunk/debian/TODO
trunk/packages/dialign/trunk/debian/changelog
trunk/packages/dialign/trunk/debian/compat
trunk/packages/dialign/trunk/debian/control
trunk/packages/dialign/trunk/debian/copyright
trunk/packages/dialign/trunk/debian/dialign.doc-base
trunk/packages/dialign/trunk/debian/dialign2-2.1.xml
trunk/packages/dialign/trunk/debian/dirs
trunk/packages/dialign/trunk/debian/docs
trunk/packages/dialign/trunk/debian/install
trunk/packages/dialign/trunk/debian/manpages
trunk/packages/dialign/trunk/debian/patches/
trunk/packages/dialign/trunk/debian/patches/00list
trunk/packages/dialign/trunk/debian/patches/20_no_DIALIGN2_DIR.dpatch
trunk/packages/dialign/trunk/debian/patches/30_local_doc.dpatch
trunk/packages/dialign/trunk/debian/rules
trunk/packages/dialign/trunk/debian/watch
Log:
Load dialign-2.1.1 into trunk/packages/dialign/trunk.
Added: trunk/packages/dialign/trunk/debian/BUGS
===================================================================
--- trunk/packages/dialign/trunk/debian/BUGS 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/BUGS 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+The manpage has an extra AUTHORS section, added by the xsl stylesheet.
Added: trunk/packages/dialign/trunk/debian/README.Debian
===================================================================
--- trunk/packages/dialign/trunk/debian/README.Debian 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/README.Debian 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,10 @@
+dialign for Debian
+------------------
+
+In order to make dialign work 'out of the box', I hard-coded the path
+of the substitution matrices to /usr/share/dialign, where the package
+installs them. Hence, it is not necessary to set the DIALIGN2_DIR
+environment variable. Setting it overrides the default path I
+hard-coded.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>, Sun, 9 Apr 2006 23:53:26 +0900
Added: trunk/packages/dialign/trunk/debian/TODO
===================================================================
--- trunk/packages/dialign/trunk/debian/TODO 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/TODO 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+Write scripts to update doc-base at installation and purge.
Added: trunk/packages/dialign/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign/trunk/debian/changelog 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/changelog 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,6 @@
+dialign (2.1.1-1) unstable; urgency=low
+
+ * Initial release Closes: #361682
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 9 Apr 2006 23:53:26 +0900
+
Added: trunk/packages/dialign/trunk/debian/compat
===================================================================
--- trunk/packages/dialign/trunk/debian/compat 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/compat 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+4
Added: trunk/packages/dialign/trunk/debian/control
===================================================================
--- trunk/packages/dialign/trunk/debian/control 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/control 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,20 @@
+Source: dialign
+Section: science
+Priority: optional
+Maintainer: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xsl
+Standards-Version: 3.6.2
+
+Package: dialign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Segment-based multiple sequence alignment
+ DIALIGN2 is a command line tool to perform multiple alignment of
+ protein or DNA sequences. It constructs alignments from gapfree pairs
+ of similar segments of the sequences. This scoring scheme for
+ alignments is the basic difference between DIALIGN and other global or
+ local alignment methods. Note that DIALIGN does not employ any kind of
+ gap penalty. It has been published by Morgenstern B. in
+ Bioinformatics. 1999 Mar;15(3):211-8.
+ .
+ Homepage: http://dialign.gobics.de/
Added: trunk/packages/dialign/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign/trunk/debian/copyright 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/copyright 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,27 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Sun, 9 Apr 2006. The packaging
+work is in the public domain unless stated otherwise. The manpage is
+licenced under the LGPL.
+
+Dialign was downloaded from http://dialign.gobics.de/download/dialign_package.tgz
+
+Written by Burkhard Morgenstern and Said Abdeddaim, 1999.
+Copyright Holder: Burkhard Morgenstern <bmorgen at gwdg.de> 1999-2005
+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 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'.
Added: trunk/packages/dialign/trunk/debian/dialign.doc-base
===================================================================
--- trunk/packages/dialign/trunk/debian/dialign.doc-base 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/dialign.doc-base 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,10 @@
+Document: dialign
+Title: Dialign User Manual
+Author: Burkhard Morgenstern
+Abstract: This manual describes how to use
+ dialign.
+Section: Apps/Science
+
+Format: text
+Files: /usr/share/doc/dialign/USER_GUIDE.gz
+
Added: trunk/packages/dialign/trunk/debian/dialign2-2.1.xml
===================================================================
--- trunk/packages/dialign/trunk/debian/dialign2-2.1.xml 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/dialign2-2.1.xml 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,456 @@
+
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
+"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>avril 9, 2006</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>DIALIGN</refentrytitle>">
+ <!ENTITY dhpackage "dialign2-2">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Multiple alignment program using the segment-to-segment approach</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>dialign2-2</command>
+
+ <arg choice="opt">options</arg>
+
+ <arg>seq_file</arg>
+ </cmdsynopsis>
+ <para><filename>seq_file</filename> is the name of the input sequence file; this must be a multiple FASTA file (all sequences in one file).</para>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para><command>&dhpackage;</command> is a program that constructs
+ alignments from gapfree pairs of similar segments of the
+ sequences. If (possibly) coding nucleic acid sequences are to be
+ aligned, DIALIGN optionally translates the compared `nucleic acid
+ segments' to `peptide segments' according to the genetic code –
+ without presupposing any of the three possible reading frames, so
+ all combinations of reading frames get checked for significant
+ similarity.</para>
+
+ <para>By default, DIALIGN creates a single file containing
+ <itemizedlist>
+ <listitem><para>An alignment of the input sequences in DIALIGN format.</para></listitem>
+ <listitem><para>The same alignment in FASTA format.</para></listitem>
+ <listitem><para>A sequence tree in PHYLIP format. This tree is constructed by applying
+ the UPGMA clustering method to the DIALIGN similarity scores. It roughly
+ reflects the different degrees of similarity among sequences. For
+ detailed phylogenetic analysis, we recommend the usual methods for
+ phylogenetic reconstruction.</para></listitem>
+ </itemizedlist>
+ </para>
+ <para>
+ The format of the output files is documented in <filename>/usr/share/doc/dialign/USER_GUIDE.gz</filename>. The FASTA, CLUSTALW and MSF output formats are optionally available (see OPTIONS).</para>
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-afc</option>
+ </term>
+ <listitem>
+ <para>Creates additional output file "*.afc" containing data of all fragments considered for alignment. WARNING: this file can be HUGE!</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-afc_v</option>
+ </term>
+ <listitem>
+ <para>Like "<option>-afc</option>" but verbose: fragments are explicitly printed. WARNING: this file can be EVEN BIGGER!</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-anc</option>
+ </term>
+ <listitem>
+ <para>Anchored alignment. Requires a file <filename>seq_file.anc</filename> containing anchor points.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-cs</option>
+ </term>
+ <listitem>
+ <para>If segments are translated, not only the `Watson strand' but also the `Crick strand' is looked at.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-cw</option>
+ </term>
+ <listitem>
+ <para>Additional output file in CLUSTAL W format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ds</option>
+ </term>
+ <listitem>
+ <para>`DNA alignment speed up'. Non-translated nucleic acid fragments are taken into account only if they start with at least two matches. Speeds up DNA alignment at the expense of sensitivity.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fa</option>
+ </term>
+ <listitem>
+ <para>Additional output file in FASTA format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ff</option>
+ </term>
+ <listitem>
+ <para>Creates file <filename>*.frg</filename> containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fn <filename>out_file</filename></option>
+ </term>
+ <listitem>
+ <para>Output files are named <filename>out_file.extension</filename>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fop</option>
+ </term>
+ <listitem>
+ <para>Creates file <filename>*.fop</filename> containing coordinates of all fragments that are part of the respective pairwise alignments.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-fsm</option>
+ </term>
+ <listitem>
+ <para>Creates file <filename>*.fsm</filename> containing coordinates of all fragments that are part of the final alignment</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-iw</option>
+ </term>
+ <listitem>
+ <para>Overlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned). This option speeds up the alignment but may lead to reduced alignment quality.
+</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-lgs</option>
+ </term>
+ <listitem>
+ <para>`Long genomic sequences' - combines the following options: <option>-ma</option>, <option>-thr <parameter>2</parameter></option>, <option>-lmax <parameter>30</parameter></option>, <option>-smin <parameter>8</parameter></option>, <option>-nta</option>, <option>-ff</option>, <option>-fop</option>, <option>-ff</option>, <option>-cs</option>, <option>-ds</option>, <option>-pst</option>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-lgs_t</option>
+ </term>
+ <listitem>
+ <para>Like "<option>-lgs</option>" but with all segment pairs assessed at the peptide level (rather than 'mixed alignments' as with the "-lgs" option). Therefore faster than -lgs but not very sensitive for non-coding regions.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-lmax <parameter>x</parameter></option>
+ </term>
+ <listitem>
+ <para>Maximum fragment length = <parameter>x</parameter> (default: <parameter>x</parameter> = 40 or <parameter>x</parameter> = 120 for `translated' fragments). Shorter <parameter>x</parameter> speeds up the program but may affect alignment quality.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-lo</option>
+ </term>
+ <listitem>
+ <para>(Long Output) Additional file <filename>*.log</filename> with information abut fragments selected for pairwise alignment and about consistency in multi-alignment proceedure.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ma</option>
+ </term>
+ <listitem>
+ <para>`mixed alignments' consisting of P-fragments and N-fragments if nucleic acid sequences are aligned.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-mask</option>
+ </term>
+ <listitem>
+ <para>Residues not belonging to selected fragments are replaced by `*' characters in output alignment (rather than being printed in lower-case characters)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-mat</option>
+ </term>
+ <listitem>
+ <para>Creates file <filename>*mat</filename> with substitution counts derived from the fragments that have been selected for alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-mat_thr <parameter>t</parameter></option>
+ </term>
+ <listitem>
+ <para>Like "-mat" but only fragments with weight score >
+ <parameter>t</parameter> are considered.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-max_link</option>
+ </term>
+ <listitem>
+ <para>"Maximum linkage" clustering used to construct sequence tree (instead of UPGMA).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-min_link</option>
+ </term>
+ <listitem>
+ <para>"Minimum linkage" clustering used.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-mot</option>
+ </term>
+ <listitem>
+ <para>"Motif" option.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-msf</option>
+ </term>
+ <listitem>
+ <para>Separate output file in <acronym>MSF</acronym> format.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-n</option>
+ </term>
+ <listitem>
+ <para>Input sequences are nucleic acid sequences. No translation
+ of fragments.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-nt</option>
+ </term>
+ <listitem>
+ <para>Input sequences are nucleic acid sequences and `nucleic acid segments' are translated to `peptide segments'.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-nta</option>
+ </term>
+ <listitem>
+ <para>`No textual alignment'. Textual alignment suppressed. This option makes sense if other output files are of intrest — e.g. the fragment files created with <option>-ff</option>, <option>-fop</option>, <option>-fsm</option> or <option>-lo</option>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-o</option>
+ </term>
+ <listitem>
+ <para>Fast version, resulting alignments may be slightly different.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ow</option>
+ </term>
+ <listitem>
+ <para>Overlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming). Warning: overlap weights generally improve alignment quality but the running time increases in the order O(n^4) with the number of sequences. This is why, by default, overlap weights are used only for sequence sets with < 36 sequences.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-pst</option>
+ </term>
+ <listitem>
+ <para>"Print status". Creates and updates a file <filename>*.sta</filename> with information about the current status of the program run. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-smin <parameter>x</parameter></option>
+ </term>
+ <listitem>
+ <para>Minimum similarity value for first residue pair (or codon pair) in fragments. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-stars <parameter>x</parameter></option>
+ </term>
+ <listitem>
+ <para>Maximum number of `*' characters indicating degree of local similarity among sequences. By default, no stars are used but numbers between 0 and 9, instead.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-stdo</option>
+ </term>
+ <listitem>
+ <para>Results written to standard output.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ta</option>
+ </term>
+ <listitem>
+ <para>Standard textual alignment printed (overrides suppression of textual alignments in special options, e.g. -lgs).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-thr <parameter>x</parameter></option>
+ </term>
+ <listitem>
+ <para>Threshold T = x.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-xfr</option>
+ </term>
+ <listitem>
+ <para>"Exclude fragments". List of fragments can be specified that are NOT considered for pairwise alignment.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+
+ <para>
+ General remark: If contradictory options are used, subsequent
+ options override previous ones, e.g.: <code>dialign2-2 -nt -n
+ <filename>seq_file</filename></code> runs the program with the
+ "-n" option (no translation!), while <code>dialign2-2 -n -nt
+ <filename>seq_file</filename></code> runs it with the "-nt"
+ option (translation!).
+ </para>
+
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>The full documentation is in <filename>/usr/share/doc/dialign/</filename>.</para>
+
+ <para>The website of dialign: http://dialign.gobics.de/</para>
+
+ <para>DIALING2 has recently be re-implemented. See http://dialign-t.gobics.de/</para>
+
+ </refsect1>
+
+ <refsect1>
+ <title>ENVIRONMENT VARIABLES</title>
+ <para>You can create an environment variable `<envar>DIALIGN2_DIR</envar>' pointing to a directory where the substitution matrices are (see FILES). When installed from the Debian package, it is not necessary to set this environnement variable to run DIALIGN.</para>
+ </refsect1>
+
+ <refsect1>
+ <title>FILES</title>
+
+ <para>DIALIGN2 needs the files <filename>tp400_dna</filename>, <filename>tp400_prot</filename>, <filename>tp400_trans</filename> and <filename>BLOSUM</filename>. When DIALIGN is installed from the Debian package, they are stored in <filename>/usr/share/dialign/</filename>.</para>
+
+ <para>DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix. In the current
+version, it is NOT possible to replace BLOSUM62 by other similarity matrices.</para>
+
+ </refsect1>
+
+
+ <refsect1>
+ <title>REFERENCE</title>
+ <para>B. Morgenstern (1999).
+ DIALIGN 2: improvement of the segment-to-segment approach to
+ multiple sequence alignment.
+ Bioinformatics 15, 211 - 218.
+
+ Public research assisted by DIALIGN should cite this article.</para>
+ </refsect1>
+
+
+ <refsect1>
+ <title>AUTHORS</title>
+
+ <para>
+ DIALIGN was written by Burkhard Morgenstern
+ <email>bmorgen at gwdg.de</email> and Said Abdeddaim at University
+ of Bielefeld (FSPM and International Graduate School in
+ Bioinformatics and Genome Research), GSF (ISG, IBB, MIPS/IBI),
+ North Carolina State University, Universite de Rouen, MPI fuer
+ Biochemie (Martinsried), University of Goettingen, Institute of
+ Microbiology and Genetics.
+ </para>
+
+ <para>This manual page was adapted from the DIALIGN manual 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; Lesser General Public License, Version 2.1 any
+ later version published by the Free Software Foundation.
+ </para>
+
+ <para>
+ On Debian systems, the complete text of the GNU Lesser General Public
+ License can be found in /usr/share/common-licenses/LGPL.
+ </para>
+
+ </refsect1>
+
+</refentry>
+
Added: trunk/packages/dialign/trunk/debian/dirs
===================================================================
--- trunk/packages/dialign/trunk/debian/dirs 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/dirs 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/dialign
Added: trunk/packages/dialign/trunk/debian/docs
===================================================================
--- trunk/packages/dialign/trunk/debian/docs 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/docs 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+USER_GUIDE
Added: trunk/packages/dialign/trunk/debian/install
===================================================================
--- trunk/packages/dialign/trunk/debian/install 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/install 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+dialign2_dir/* usr/share/dialign
Added: trunk/packages/dialign/trunk/debian/manpages
===================================================================
--- trunk/packages/dialign/trunk/debian/manpages 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/manpages 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1 @@
+dialign2-2.1
Added: trunk/packages/dialign/trunk/debian/patches/00list
===================================================================
--- trunk/packages/dialign/trunk/debian/patches/00list 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/patches/00list 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,2 @@
+20_no_DIALIGN2_DIR.dpatch
+30_local_doc.dpatch
Added: trunk/packages/dialign/trunk/debian/patches/20_no_DIALIGN2_DIR.dpatch
===================================================================
--- trunk/packages/dialign/trunk/debian/patches/20_no_DIALIGN2_DIR.dpatch 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/patches/20_no_DIALIGN2_DIR.dpatch 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,38 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 20_no_DIALIGN2_DIR.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+## This patch is hereby released in public domain.
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Gives a default value to par_file so that the environment variable
+## DP: DIALIGN2_DIR is optional
+
+ at DPATCH@
+
+--- dialign_package_old/src/dialign.c 2005-02-22 01:32:55.000000000 +0900
++++ dialign_package/src/dialign.c 2006-04-09 23:14:18.000000000 +0900
+@@ -296,10 +296,13 @@
+
+ if ((par_file = getenv(dialign_dir)) == NULL)
+ {
+- printf("\n \n \n Please set the environmentvariable DIALIGN2_DIR \n");
+- printf(" as described in the README file \n");
+- exit(1);
+- }
++ par_file = "/usr/share/dialign/" ; /* Default value for Debian, makes the environment variable optional */
++
++/* printf("\n \n \n Please set the environmentvariable DIALIGN2_DIR \n");
++ * printf(" as described in the README file \n");
++ * exit(1);
++ */
++ }
+
+ argnum = argc;
+
+@@ -523,6 +526,7 @@
+ printf(" to a directory containing the files \n\n");
+ printf(" BLOSUM \n tp400_dna\n tp400_prot \n tp400_trans \n\n" );
+ printf(" These files should be contained in the DIALIGN package \n\n\n" ) ;
++ printf(" See /usr/share/doc/dialign/README.Debian for more details \n" ) ;
+ exit(1) ;
+
+
Property changes on: trunk/packages/dialign/trunk/debian/patches/20_no_DIALIGN2_DIR.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/dialign/trunk/debian/patches/30_local_doc.dpatch
===================================================================
--- trunk/packages/dialign/trunk/debian/patches/30_local_doc.dpatch 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/patches/30_local_doc.dpatch 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,21 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 30_local_doc.dpatch by Charles Plessy <charles-debian-nospam at plessy.org>
+## This patch is hereby released in the public domain.
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Mentions the man page and /usr/share/doc/dialign when it is invoked
+## DP: without arguments
+
+ at DPATCH@
+
+--- dialign_package_old/src/dialign.c 2006-04-16 21:34:22.000000000 +0900
++++ dialign_package/src/dialign.c 2006-04-16 21:41:00.000000000 +0900
+@@ -320,7 +320,7 @@
+ printf(" -lgs long genomic sequences: Both nucleotide and peptide\n");
+ printf(" similarities calculated \n\n");
+ printf(" Many more options are available, please consult the \n");
+- printf(" DIALIGN USER_GUIDE that should come with the DIALIGN package.\n");
++ printf(" DIALIGN USER_GUIDE in /usr/share/doc/dialign/, or the manpage.\n");
+ printf(" For more information on DIALIGN, please visit the DIALIGN\n");
+ printf(" home page at BiBiServ (Bielefeld Bioinformatic Server): \n\n") ;
+ printf(" http://bibiserv.techfak.uni-bielefeld.de/dialign/ \n\n");
Property changes on: trunk/packages/dialign/trunk/debian/patches/30_local_doc.dpatch
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/dialign/trunk/debian/rules
===================================================================
--- trunk/packages/dialign/trunk/debian/rules 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/rules 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,74 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package dialign.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+# Modifications by Charles Plessy during the year 2006
+# are hereby released as "public domain".
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+patch:
+ dpatch apply-all
+ dpatch cat-all --desc-only > patch-stamp
+
+unpatch:
+ dpatch deapply-all
+ rm -rf patch-stamp debian/patched
+
+build: patch build-stamp
+
+build-stamp:
+ dh_testdir
+ $(MAKE) -C src
+ xsltproc -''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl debian/dialign2-2.1.xml
+ touch build-stamp
+
+clean: clean-patched unpatch
+
+clean-patched:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ find src/ -name '*.o' -exec rm {} \;
+ find src/ -name dialign2-2 -exec rm {} \;
+ find . -name dialign2-2.1 -exec rm {} \;
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ install -o 755 src/dialign2-2 debian/dialign/usr/bin/
+
+binary-indep: build install
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install
+ dh_installman
+ 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
Property changes on: trunk/packages/dialign/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/dialign/trunk/debian/watch
===================================================================
--- trunk/packages/dialign/trunk/debian/watch 2006-04-18 12:56:20 UTC (rev 18)
+++ trunk/packages/dialign/trunk/debian/watch 2006-04-18 12:58:15 UTC (rev 19)
@@ -0,0 +1,2 @@
+version=3
+http://dialign.gobics.de/download/dialign_package.tgz
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