[med-svn] r226 - trunk/packages/amap-align/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Mar 10 06:18:34 CET 2007
Author: charles-guest
Date: 2007-03-10 05:18:34 +0000 (Sat, 10 Mar 2007)
New Revision: 226
Added:
trunk/packages/amap-align/trunk/debian/NEWS
trunk/packages/amap-align/trunk/debian/amap.1.xml
Removed:
trunk/packages/amap-align/trunk/debian/README.Debian
trunk/packages/amap-align/trunk/debian/amap-align.1.xml
trunk/packages/amap-align/trunk/debian/dirs
trunk/packages/amap-align/trunk/debian/install
trunk/packages/amap-align/trunk/debian/manpages
Modified:
trunk/packages/amap-align/trunk/debian/changelog
trunk/packages/amap-align/trunk/debian/control
trunk/packages/amap-align/trunk/debian/rules
Log:
moving /usr/bin/amap-align to /usr/bin/amap
Added: trunk/packages/amap-align/trunk/debian/NEWS
===================================================================
--- trunk/packages/amap-align/trunk/debian/NEWS 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/NEWS 2007-03-10 05:18:34 UTC (rev 226)
@@ -0,0 +1,11 @@
+amap-align (2.0-2) unstable; urgency=low
+
+Previous versions of the package amap-align were shipping the program under a
+binary name (amap-align) which differed from the original one (amap) because
+there was already an amap program in Debian. Since this program has been
+removed from the Etch distribution, amap-align now provides its function
+through the program /usr/bin/align. To help the transition, a symbolic link,
+/usr/bin/amap-align, is provided, but may be supressed in the releases
+following Etch.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 12:59:02 +0900
Deleted: trunk/packages/amap-align/trunk/debian/README.Debian
===================================================================
--- trunk/packages/amap-align/trunk/debian/README.Debian 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/README.Debian 2007-03-10 05:18:34 UTC (rev 226)
@@ -1,7 +0,0 @@
-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
Deleted: trunk/packages/amap-align/trunk/debian/amap-align.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap-align.1.xml 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/amap-align.1.xml 2007-03-10 05:18:34 UTC (rev 226)
@@ -1,267 +0,0 @@
-<?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 another 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 progressive 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 reordering 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>
Copied: trunk/packages/amap-align/trunk/debian/amap.1.xml (from rev 220, trunk/packages/amap-align/trunk/debian/amap-align.1.xml)
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap-align.1.xml 2007-02-26 14:15:15 UTC (rev 220)
+++ trunk/packages/amap-align/trunk/debian/amap.1.xml 2007-03-10 05:18:34 UTC (rev 226)
@@ -0,0 +1,273 @@
+<?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>amap</refname>
+
+ <refpurpose>Protein multiple alignment by sequence annealing</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>amap</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>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 progressive 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 reordering 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>
+ NOTE
+ </title>
+
+ <para>In older versions ( < 2.0-1) of the package for &debian; systems, the <command>amap</command> command was renamed <command>amap-align</command> because there was already another tool called <command>amap</command> (which performs some computer network diagnostics). A symbolic link <command>amap-align</command> is still provided for upgrade purposes but will be removed in Debian releases posterior to Etch (Debian 4.0).</para>
+ </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>
Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/changelog 2007-03-10 05:18:34 UTC (rev 226)
@@ -2,8 +2,9 @@
* Add Subversion repository URL to debian/control.
* Patching for building with gcc-4.3. Many thanks to Martin Michlmayr (Closes:413477)
+ * Renaming /usr/bin/amap-align to /usr/bin/amap
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 12:41:06 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 13:46:04 +0900
amap-align (2.0-1) unstable; urgency=low
Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/control 2007-03-10 05:18:34 UTC (rev 226)
@@ -1,6 +1,7 @@
Source: amap-align
Section: science
Priority: optional
+Conflicts: amap ( <= 4.8-1 )
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
Deleted: trunk/packages/amap-align/trunk/debian/dirs
===================================================================
--- trunk/packages/amap-align/trunk/debian/dirs 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/dirs 2007-03-10 05:18:34 UTC (rev 226)
@@ -1 +0,0 @@
-usr/bin
Deleted: trunk/packages/amap-align/trunk/debian/install
===================================================================
--- trunk/packages/amap-align/trunk/debian/install 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/install 2007-03-10 05:18:34 UTC (rev 226)
@@ -1 +0,0 @@
-amap usr/bin/amap-align
Deleted: trunk/packages/amap-align/trunk/debian/manpages
===================================================================
--- trunk/packages/amap-align/trunk/debian/manpages 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/manpages 2007-03-10 05:18:34 UTC (rev 226)
@@ -1 +0,0 @@
-debian/amap-align.1
Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules 2007-03-10 03:44:12 UTC (rev 225)
+++ trunk/packages/amap-align/trunk/debian/rules 2007-03-10 05:18:34 UTC (rev 226)
@@ -21,7 +21,7 @@
build: patch
dh_testdir
- $(XP) $(DB2MAN) debian/amap-align.1.xml
+ $(XP) $(DB2MAN) debian/amap.1.xml
$(MAKE)
touch build-stamp
@@ -38,14 +38,13 @@
dh_testroot
rm -f build-stamp
-$(MAKE) clean
- dh_clean debian/amap-align.1
+ dh_clean debian/amap.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
@@ -55,9 +54,10 @@
dh_installchangelogs
dh_installdocs
dh_installexamples
-# dh_install
- dh_installman
- dh_link
+ dh_install amap usr/bin/
+ dh_installman debian/amap.1
+ dh_link usr/bin/amap usr/bin/amap-align \
+ usr/share/man/man1/amap.1 usr/share/man/man1/amap-align.1
dh_strip
dh_compress
dh_fixperms
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