[med-svn] r78 - in trunk/packages/amap-align/trunk: . debian
debian/patches
Charles Plessy
charles-guest at costa.debian.org
Sun Jul 9 07:35:27 UTC 2006
Author: charles-guest
Date: 2006-07-09 07:35:24 +0000 (Sun, 09 Jul 2006)
New Revision: 78
Added:
trunk/packages/amap-align/trunk/debian/
trunk/packages/amap-align/trunk/debian/README.Debian
trunk/packages/amap-align/trunk/debian/amap-align.1
trunk/packages/amap-align/trunk/debian/amap-align.1.xml
trunk/packages/amap-align/trunk/debian/changelog
trunk/packages/amap-align/trunk/debian/compat
trunk/packages/amap-align/trunk/debian/control
trunk/packages/amap-align/trunk/debian/copyright
trunk/packages/amap-align/trunk/debian/dirs
trunk/packages/amap-align/trunk/debian/docs
trunk/packages/amap-align/trunk/debian/install
trunk/packages/amap-align/trunk/debian/manpages
trunk/packages/amap-align/trunk/debian/patches/
trunk/packages/amap-align/trunk/debian/patches/00list
trunk/packages/amap-align/trunk/debian/patches/10_rename-amap
trunk/packages/amap-align/trunk/debian/rules
trunk/packages/amap-align/trunk/debian/watch
Removed:
trunk/packages/amap-align/trunk/amap
Log:
Load amap-align-2.0 into trunk/packages/amap-align/trunk.
Deleted: trunk/packages/amap-align/trunk/amap
===================================================================
(Binary files differ)
Added: trunk/packages/amap-align/trunk/debian/README.Debian
===================================================================
--- trunk/packages/amap-align/trunk/debian/README.Debian 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/README.Debian 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,7 @@
+amap-align for Debian
+---------------------
+
+On Debian systems, the amap program has been renamed amap-align because there
+was already another program called amap in our archives.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>, Sun, 9 Jul 2006 12:53:25 +0900
Added: trunk/packages/amap-align/trunk/debian/amap-align.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap-align.1 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/amap-align.1 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,152 @@
+.\"Generated by db2man.xsl. Don't modify this, modify the source.
+.de Sh \" Subsection
+.br
+.if t .Sp
+.ne 5
+.PP
+\fB\\$1\fR
+.PP
+..
+.de Sp \" Vertical space (when we can't use .PP)
+.if t .sp .5v
+.if n .sp
+..
+.de Ip \" List item
+.br
+.ie \\n(.$>=3 .ne \\$3
+.el .ne 3
+.IP "\\$1" \\$2
+..
+.TH "AMAP" 1 "mai 3, 2006" "" ""
+.SH NAME
+amap-align \- Protein multiple alignment by sequence annealing
+.SH "SYNOPSIS"
+.ad l
+.hy 0
+.HP 11
+\fBamap\-align\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR]
+.ad
+.hy
+
+.SH "DESCRIPTION"
+
+.PP
+On Debian™ systems, the \fBamap\fR command has been renamed \fBamap\-align\fR because there was already anonther tool called \fBamap\fR (which performs some computer network diagnostics)
+
+.PP
+AMAP is a tool to perform multiple alignment of peptidic sequences\&. It utilizes posterior decoding, and a sequence\-annealing alignment, instead of the traditional progressive alignment method\&. It is the only alignment program that allows to control the sensitivity / specificity tradeoff\&. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation\&.
+
+.PP
+In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score \- a new alignment accuracy measure, based on a metric for the multiple\-alignment space, which integrates sensitivity and specificity into a single balanced measure\&. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences\&.
+
+.PP
+\fBamap\-align\fR aligns sequences provided in MFA format\&. This format consists of multiple sequences\&. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\&. The description line is distinguished from the sequence data by a greater\-than (``>'') symbol in the first column\&.
+
+.SH "OPTIONS"
+
+.TP
+\fB\-clustalw\fR
+use CLUSTALW output format instead of MFA
+
+.TP
+\fB\-c\fR \fB\-\-consistency\fR \fIREPS\fR
+use 0 <= \fIREPS\fR <= 5 (default: 0) passes of consistency transformation
+
+.TP
+\fB\-ir\fR \fB\-\-iterative\-refinement\fR \fIREPS\fR
+use 0 <= \fIREPS\fR <=1000 (default: 0) passes of iterative\-refinement
+
+.TP
+\fB\-pre\fR \fB\-\-pre\-training\fR \fIREPS\fR
+use 0 <= \fIREPS\fR <= 20 (default: 0) rounds of pretraining
+
+.TP
+\fB\-pairs\fR
+generate all\-pairs pairwise alignments
+
+.TP
+\fB\-viterbi\fR
+use Viterbi algorithm to generate all pairs (automatically enables \fB\-pairs\fR)
+
+.TP
+\fB\-v\fR \fB\-\-verbose\fR
+Report progress while aligning (default: off)
+
+.TP
+\fB\-annot\fR \fIFILENAME\fR
+write annotation for multiple alignment to \fIFILENAME\fR
+
+.TP
+\fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR
+compute EM transition probabilities, store in \fIFILENAME\fR (default: no training)
+
+.TP
+\fB\-e\fR \fB\-\-emissions\fR
+also reestimate emission probabilities (default: off)
+
+.TP
+\fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR
+read parameters from \fIFILENAME\fR (default: )
+
+.TP
+\fB\-a\fR \fB\-\-alignment\-order\fR
+print sequences in alignment order rather than input order (default: off)
+
+.TP
+\fB\-g\fR \fB\-\-gap\-factor\fR \fIGF\fR
+use \fIGF\fR as the gap\-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0\&.5)
+
+.TP
+\fB\-w\fR \fB\-\-edge\-weight\-threshold\fR \fIW\fR
+stop the sequence annealing process when best edge has lower weight than \fIW\fR, set to 0 for best sensitivity, higher values for better specificity (default: 0)
+
+.TP
+\fB\-prog\fR \fB\-\-progressive\fR
+use progresive alignment instead of sequence annealing alignment (default: off)
+
+.TP
+\fB\-noreorder\fR \fB\-\-no\-edge\-reordering\fR
+disable reordring of edges during sequence annealing alignment (default: off)
+
+.TP
+\fB\-maxstep\fR \fB\-\-use\-max\-stepsize\fR
+use maximum improvement step size instead of tGf edge ranking (default: off)
+
+.TP
+\fB\-print\fR \fB\-\-print\-posteriors\fR
+only print the posterior probability matrices (default: off)
+
+.SH "SEE ALSO"
+
+.PP
+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 \fI/usr/share/doc/amap\-align/\fR)\&. Future releases might implement the algorithm using a new independent code base\&. On Debian™ systems, PROBCONS is available in the probcons package\&.
+
+.SH "REFERENCES"
+
+.PP
+For more details on AMAP and AMA, see Schwartz, Ariel S\&., Myers, Eugene W\&., and Pachter, Lior\&. Alignment Metric Accuracy (Submitted for publication)\&. For more details on sequence\-annealing, see Schwartz, Ariel S\&. and Pachter, Lior\&. Multiple Alignment by Sequence Annealing (Submitted for publication)\&.
+
+.PP
+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\&.
+
+.SH "AUTHORS"
+
+.TP 3
+\(bu
+PROBCONS was written by Chuong Do\&.
+.TP
+\(bu
+AMAP algorithm implemented by Ariel Schwartz (<sariel at cs\&.berkeley\&.edu>)\&.
+.TP
+\(bu
+This manual page was written by Charles Plessy <charles\-debian\-nospam at plessy\&.org> for the Debian™ system (but may be used by others)\&.
+.LP
+
+.SH "LICENCE"
+
+.PP
+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\&.
+
+.PP
+This manpage is hereby placed in the public domain\&.
+
Added: trunk/packages/amap-align/trunk/debian/amap-align.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap-align.1.xml 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/amap-align.1.xml 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,267 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//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 dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>AMAP</refentrytitle>">
+ <!ENTITY dhpackage "amap-align">
+ <!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>Protein multiple alignment by sequence annealing</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+
+ <arg choice="opt"><option><replaceable>OPTION</replaceable></option></arg>
+
+ <arg><replaceable>MFAFILE</replaceable></arg>
+ <arg choice="opt"><replaceable>MFAFILE</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>On &debian; systems, the <command>amap</command> command has been renamed <command>amap-align</command> because there was already anonther tool called <command>amap</command> (which performs some computer network diagnostics)</para>
+
+ <para>AMAP is a tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.</para>
+
+ <para>In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - a new alignment accuracy measure, based on a metric for the multiple-alignment space, which integrates sensitivity and specificity into a single balanced measure. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences.</para>
+
+ <para><command>&dhpackage;</command> aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (<quote>></quote>) symbol in the first column.</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-clustalw</option>
+ </term>
+ <listitem>
+ <para>use CLUSTALW output format instead of MFA</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-c</option>
+ <option>--consistency</option> <varname>REPS</varname>
+ </term>
+ <listitem>
+ <para>use 0 <= <varname>REPS</varname> <= 5 (default: 0) passes of consistency transformation</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-ir</option>
+ <option>--iterative-refinement</option> <varname>REPS</varname>
+ </term>
+ <listitem>
+ <para>use 0 <= <varname>REPS</varname> <=1000 (default: 0) passes of iterative-refinement</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-pre</option>
+ <option>--pre-training</option> <varname>REPS</varname>
+ </term>
+ <listitem>
+ <para>use 0 <= <varname>REPS</varname> <= 20 (default: 0) rounds of pretraining</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-pairs</option>
+ </term>
+ <listitem>
+ <para>generate all-pairs pairwise alignments</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-viterbi</option>
+ </term>
+ <listitem>
+ <para>use Viterbi algorithm to generate all pairs (automatically enables <option>-pairs</option>)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-v</option>
+ <option>--verbose</option>
+ </term>
+ <listitem>
+ <para>Report progress while aligning (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-annot</option> <filename>FILENAME</filename> </term>
+ <listitem>
+ <para>write annotation for multiple alignment to <filename>FILENAME</filename></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-t</option>
+ <option>--train</option> <filename>FILENAME</filename>
+ </term>
+ <listitem>
+ <para>compute EM transition probabilities, store in <filename>FILENAME</filename> (default: no training)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-e</option>
+ <option>--emissions</option>
+ </term>
+ <listitem>
+ <para>also reestimate emission probabilities (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-p</option>
+ <option>--paramfile</option> <filename>FILENAME</filename>
+ </term>
+ <listitem>
+ <para>read parameters from <filename>FILENAME</filename> (default: )</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-a</option>
+ <option>--alignment-order</option>
+ </term>
+ <listitem>
+ <para>print sequences in alignment order rather than input order (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-g</option>
+ <option>--gap-factor</option>
+ <varname>GF</varname>
+ </term>
+ <listitem>
+ <para>use <varname>GF</varname> as the gap-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0.5)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-w</option>
+ <option>--edge-weight-threshold</option>
+ <varname>W</varname>
+ </term>
+ <listitem>
+ <para>stop the sequence annealing process when best edge has lower weight than <varname>W</varname>, set to 0 for best sensitivity, higher values for better specificity (default: 0)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-prog</option>
+ <option>--progressive</option>
+ </term>
+ <listitem>
+ <para>use progresive alignment instead of sequence annealing alignment (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-noreorder</option>
+ <option>--no-edge-reordering</option>
+ </term>
+ <listitem>
+ <para>disable reordring of edges during sequence annealing alignment (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-maxstep</option>
+ <option>--use-max-stepsize</option>
+ </term>
+ <listitem>
+ <para>use maximum improvement step size instead of tGf edge ranking (default: off)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-print</option>
+ <option>--print-posteriors</option>
+ </term>
+ <listitem>
+ <para>only print the posterior probability matrices (default: off)</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <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>
+ </refsect1>
+
+ <refsect1>
+ <title>REFERENCES</title>
+ <para>
+ For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for publication). For more details on sequence-annealing, see Schwartz, Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing (Submitted for publication).
+ </para>
+
+ <para>
+ 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>
Added: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/changelog 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,6 @@
+amap-align (2.0-1) unstable; urgency=low
+
+ * Initial release Closes: #366321
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 9 Jul 2006 12:53:25 +0900
+
Added: trunk/packages/amap-align/trunk/debian/compat
===================================================================
--- trunk/packages/amap-align/trunk/debian/compat 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/compat 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1 @@
+5
Added: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/control 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,22 @@
+Source: amap-align
+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), xsltproc, docbook-xml, docbook-xsl, dpatch
+Standards-Version: 3.7.2
+
+Package: amap-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Protein multiple alignment by sequence annealing
+ AMAP is a command line tool to perform multiple alignment of peptidic
+ sequences. It utilizes posterior decoding, and a sequence-annealing
+ alignment, instead of the traditional progressive alignment method. It
+ is the only alignment program that allows to control the sensitivity /
+ specificity tradeoff. It is based on the ProbCons source code, but
+ uses alignment metric accuracy and eliminates the consistency
+ transformation.
+ .
+ Homepage: http://bio.math.berkeley.edu/amap/
+
Added: trunk/packages/amap-align/trunk/debian/copyright
===================================================================
--- trunk/packages/amap-align/trunk/debian/copyright 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/copyright 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,30 @@
+This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org>
+on Sun, 9 Jul 2006 12:53:25 +0900. The packaging and the manpages work are in
+the public domain unless stated otherwise.
+
+
+AMAP was downloaded from http://bio.math.berkeley.edu/amap/download
+
+AMAP is copyright (C) 2005-2006 Ariel Schwartz <sariel at cs.berkeley.edu>
+
+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).
+
+AMAP has been made freely available as PUBLIC DOMAIN software and hence is
+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 is distributed WITHOUT WARRANTY, express or implied. The
+authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on
+the program.
+
+
+PROBCONS is copyright (C) 2004 Chuong Do <chuongdo at cs.stanford.edu>
+
+PROBCONS has been made freely available as PUBLIC DOMAIN software and
+hence is 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. PROBCONS is distributed WITHOUT WARRANTY, express or
+implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
+due to reliance on the program.
+
Added: trunk/packages/amap-align/trunk/debian/dirs
===================================================================
--- trunk/packages/amap-align/trunk/debian/dirs 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/dirs 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/amap-align/trunk/debian/docs
===================================================================
--- trunk/packages/amap-align/trunk/debian/docs 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/docs 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,2 @@
+PROBCONS.README
+README
Added: trunk/packages/amap-align/trunk/debian/install
===================================================================
--- trunk/packages/amap-align/trunk/debian/install 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/install 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1 @@
+amap usr/bin/amap-align
Added: trunk/packages/amap-align/trunk/debian/manpages
===================================================================
--- trunk/packages/amap-align/trunk/debian/manpages 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/manpages 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1 @@
+debian/amap-align.1
Added: trunk/packages/amap-align/trunk/debian/patches/00list
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/00list 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/patches/00list 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1 @@
+10_rename-amap
Added: trunk/packages/amap-align/trunk/debian/patches/10_rename-amap
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/10_rename-amap 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/patches/10_rename-amap 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,25 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 10_rename-amap.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: Rename amap to amap-align
+
+ at DPATCH@
+
+--- amap-2.0/Amap.cc 2006-04-07 06:41:21.000000000 +0900
++++ amap-align-2.0/Amap.cc 2006-07-09 14:43:13.000000000 +0900
+@@ -625,7 +625,12 @@
+ << "files README and README.PROBCONS for details." << endl
+ << endl
+ << "Usage:" << endl
+- << " amap [OPTION]... [MFAFILE]..." << endl
++ << " amap-align [OPTION]... [MFAFILE]..." << endl
++ << endl
++ << "Note:" << endl
++ << "On Debian systems, amap is renamed amap-align because there is already" << endl
++ << "an amap program in our archives. On other systems, it is possible that " << endl
++ << "you will find this program under its original amap name." << endl
+ << endl
+ << "Description:" << endl
+ << " Align sequences in MFAFILE(s) and print result to standard output" << endl
Property changes on: trunk/packages/amap-align/trunk/debian/patches/10_rename-amap
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/rules 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,71 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package probcons
+# 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 can also
+# be used without restriction.
+
+DB2MAN = "/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl"
+XP = xsltproc -o debian/ -''-nonet
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+build: patch
+ dh_testdir
+ $(XP) $(DB2MAN) debian/amap-align.1.xml
+ $(MAKE)
+ touch build-stamp
+
+patch:
+ dpatch apply-all
+ dpatch cat-all --desc-only > patch-stamp
+
+unpatch:
+ dpatch deapply-all
+ rm -rf patch-stamp debian/patched
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ -$(MAKE) clean
+ dh_clean debian/probcons.1
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ install amap debian/amap-align/usr/bin/amap-align
+
+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/amap-align/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/amap-align/trunk/debian/watch
===================================================================
--- trunk/packages/amap-align/trunk/debian/watch 2006-07-09 07:32:02 UTC (rev 77)
+++ trunk/packages/amap-align/trunk/debian/watch 2006-07-09 07:35:24 UTC (rev 78)
@@ -0,0 +1,4 @@
+version=3
+
+http://bio.math.berkeley.edu/amap/download/ amap.(\d+).(\d+).tar.gz
+
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