[med-svn] r1093 - in trunk/packages/mummer: tags tags/3.20-2 tags/3.20-2/debian tags/3.20-2/debian/patches trunk/debian

tille at alioth.debian.org tille at alioth.debian.org
Thu Jan 10 15:41:04 UTC 2008


Author: tille
Date: 2008-01-10 15:41:04 +0000 (Thu, 10 Jan 2008)
New Revision: 1093

Added:
   trunk/packages/mummer/tags/3.20-2/
   trunk/packages/mummer/tags/3.20-2/debian/
   trunk/packages/mummer/tags/3.20-2/debian/changelog
   trunk/packages/mummer/tags/3.20-2/debian/compat
   trunk/packages/mummer/tags/3.20-2/debian/control
   trunk/packages/mummer/tags/3.20-2/debian/copyright
   trunk/packages/mummer/tags/3.20-2/debian/get-orig-source
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.README.Debian
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.dirs
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.doc-base
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.docs
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.install
   trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.links
   trunk/packages/mummer/tags/3.20-2/debian/mummer.1
   trunk/packages/mummer/tags/3.20-2/debian/mummer.README.Debian
   trunk/packages/mummer/tags/3.20-2/debian/mummer.desktop
   trunk/packages/mummer/tags/3.20-2/debian/mummer.dirs
   trunk/packages/mummer/tags/3.20-2/debian/mummer.docs
   trunk/packages/mummer/tags/3.20-2/debian/mummer.install
   trunk/packages/mummer/tags/3.20-2/debian/mummer.links
   trunk/packages/mummer/tags/3.20-2/debian/mummer.manpages
   trunk/packages/mummer/tags/3.20-2/debian/patches/
   trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_docs.diff
   trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_kurtz.diff
   trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_tigr.diff
   trunk/packages/mummer/tags/3.20-2/debian/patches/02at_Makefile.diff
   trunk/packages/mummer/tags/3.20-2/debian/patches/02at_docs_web.diff
   trunk/packages/mummer/tags/3.20-2/debian/patches/02at_scripts.diff
   trunk/packages/mummer/tags/3.20-2/debian/rules
   trunk/packages/mummer/tags/3.20-2/debian/watch
Modified:
   trunk/packages/mummer/trunk/debian/changelog
   trunk/packages/mummer/trunk/debian/control
   trunk/packages/mummer/trunk/debian/mummer.desktop
   trunk/packages/mummer/trunk/debian/mummer.install
Log:
Tagged 3.20-2


Added: trunk/packages/mummer/tags/3.20-2/debian/changelog
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/changelog	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/changelog	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,42 @@
+mummer (3.20-2) unstable; urgency=low
+
+  [ Charles Plessy ]
+  * XS-DM-Upload-Allowed: Yes
+
+  [ Steffen Moeller ]
+  * Changed e-mail address in uploaders
+  * Stripped long description of mummer-doc
+
+  [ Andreas Tille ]
+  * Do not install mummer.desktop because it is a command line
+    application (Fixed debian/mummer.desktop anyway)
+  * Standards-Version: 3.7.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org>  Thu, 10 Jan 2008 12:13:24 +0100
+
+mummer (3.20-1) unstable; urgency=low
+
+  * New upstream version
+  * Fixed watch file (Thanks to Nelson A. de Oliveira <naoliv at gmail.com>)
+    Closes: #450211
+  * Do not autogenerate debian/control
+  * debian/rules: get-orig-source target that removes non-free docs
+  * debian/rules: Fixed building docs
+  * Separated patches tigr and kurtz; better Makefile for scripts
+  * Added manpage link for dnadiff and mentioned dnadiff in debian/mummer.1
+  * Used "Office" as main Freedesktop.Org category (not sure whether this
+    is a really good choice)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 07 Nov 2007 13:25:34 +0100
+
+mummer (3.19-1) unstable; urgency=low
+
+  * Initial Release (Closes: Bug#201761).
+    Thanks to Steffen Moeller <moeller at inb.uni-luebeck.de> who
+    prepared a package for version 3.17 and just some
+    cleanups were left.
+  * New Standards-Version (no changes needed)
+  * Switched to cdbs to simplify handling of patches
+  * debian/compat: 5
+
+ -- Andreas Tille <tille at debian.org>  Mon, 07 May 2007 14:11:09 +0200

Added: trunk/packages/mummer/tags/3.20-2/debian/compat
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/compat	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/compat	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1 @@
+5

Added: trunk/packages/mummer/tags/3.20-2/debian/control
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/control	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/control	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,34 @@
+Source: mummer
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+XS-DM-Upload-Allowed: Yes
+Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>
+Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
+Standards-Version: 3.7.3
+Homepage: http://mummer.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mummer
+
+Package: mummer
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk, csh
+Description: Efficient sequence alignment of full genomes
+ MUMmer is a system for rapidly aligning entire genomes, whether
+ in complete or draft form. For example, MUMmer 3.0 can find all
+ 20-basepair or longer exact matches between a pair of 5-megabase genomes
+ in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
+ computer. MUMmer can also align incomplete genomes; it handles the 100s
+ or 1000s of contigs from a shotgun sequencing project with ease, and
+ will align them to another set of contigs or a genome using the NUCmer
+ program included with the system. If the species are too divergent for
+ DNA sequence alignment to detect similarity, then the PROmer program
+ can generate alignments based upon the six-frame translations of both
+ input sequences.
+
+Package: mummer-doc
+Architecture: all
+Section: doc
+Description: Documentation for MUMmer
+ This package contains the documentation for MUMmer, a system for rapidly
+ aligning entire genomes.

Added: trunk/packages/mummer/tags/3.20-2/debian/copyright
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/copyright	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/copyright	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,26 @@
+This package was debianized by Steffen Moeller <moeller at inb.uni-luebeck.de> on
+Sat, 21 May 2005 22:14:31 +0200.
+
+It was downloaded from http://mummer.sourceforge.net
+
+Copyright: This software is copyright (c) 2000-2007
+Copyright Holder: Stefan Kurtz <kurtz at zbh.uni-hamburg.de>,
+                  A. Phillippy <aphillip at tigr.edu>,
+                  A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and
+		  Steven L. Salzberg <salzberg at umd.edu>
+
+License:
+
+    This program is free software; you can redistribute it and/or modify it
+    under the terms of the "Artistic License" which comes with Debian.
+
+    THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED 
+    WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES 
+    OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+On Debian systems, the complete text of the Artistic License 
+can be found in `/usr/share/common-licenses/Artistic'.
+
+The Debian packaging is (C) 2005-2007, Steffen Moeller <moeller at inb.uni-luebeck.de>, 
+and Andreas Tille <tille at debian.org> and is licensed under the GPL which is
+available at `/usr/share/common-licenses/GPL'.

Added: trunk/packages/mummer/tags/3.20-2/debian/get-orig-source
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/get-orig-source	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/get-orig-source	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,13 @@
+VERSION=3.20
+NAME=mummer
+
+TARBALL=MUMmer${VERSION}.tar.gz
+wget http://belnet.dl.sourceforge.net/sourceforge/${NAME}/${TARBALL}
+rm -rf tmp
+mkdir tmp
+cd tmp
+tar -xzf ../${TARBALL}
+rm -f `find . -maxdepth 4 -name [MX]*.pdf`
+GZIP=-9 tar -czf ../${NAME}_${VERSION}.orig.tar.gz *
+cd ..
+rm -rf tmp

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.README.Debian
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.README.Debian	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.README.Debian	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,15 @@
+mummer for Debian
+-----------------
+
+The original tarball contained four papers about MUMmer in PDF
+format.  Because we have neither an explicite license nor the
+source of these PDFs they were removed from the tarball.  All
+these papers are published at
+
+    http://mummer.sourceforge.net/
+
+See the paragraphs "Applications" and "References".  The index.html
+file in the mummer-doc package is a copy of the URL above and the
+links were adjusted to point to the external copy.
+
+ -- Andreas Tille <tille at debian.org>, Mon, 7 May 2007 14:46:27 +0200

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.dirs
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.dirs	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.dirs	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1 @@
+usr/share/doc/mummer-doc

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.doc-base
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.doc-base	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.doc-base	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,21 @@
+Document: mummer-doc
+Title: MUMmer user manual
+Author: Arthur L. Delcher, Stefan Kurtz and others
+Abstract: MUMmer is a system for rapidly aligning entire genomes, whether in
+ complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or
+ longer exact matches between a pair of 5-megabase genomes in 13.7 seconds,
+ using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also
+ align incomplete genomes; it handles the 100s or 1000s of contigs from a
+ shotgun sequencing project with ease, and will align them to another set of
+ contigs or a genome using the NUCmer program included with the system. If the
+ species are too divergent for DNA sequence alignment to detect similarity, then the
+ PROmer program can generate alignments based upon the six-frame translations of both
+ input sequences.
+Section: science
+
+Format: pdf
+Files: /usr/share/doc/mummer-doc/*.pdf /usr/share/doc/mummer-doc/*.pdf
+
+Format: HTML
+Index: /usr/share/doc/mummer-doc/html/index.html
+Files: /usr/share/doc/mummer-doc/html/*.html

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.docs
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.docs	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.docs	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,2 @@
+docs/*.README
+docs/*.pdf

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.install
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.install	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.install	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1 @@
+docs/web/* usr/share/doc/mummer-doc/html

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.links
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.links	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer-doc.links	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1 @@
+usr/share/doc/mummer-doc/html/examples usr/share/doc/mummer-doc/examples

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.1
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.1	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.1	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,477 @@
+.\"                                      Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
+.\" other parameters are allowed: see man(7), man(1)
+.TH MUMMER 1 "May 21, 2005"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh        disable hyphenation
+.\" .hy        enable hyphenation
+.\" .ad l      left justify
+.\" .ad b      justify to both left and right margins
+.\" .nf        disable filling
+.\" .fi        enable filling
+.\" .br        insert line break
+.\" .sp <n>    insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+mummer \- package for sequence alignment of multiple genomes
+.SH SYNOPSIS
+.B mummer-annotate
+.RI <gapfile> <datafile> 
+.br
+.B combineMUMs
+.RI <RefSequence> <MatchSequences> <GapsFile>
+.br
+.B delta-filter
+.RI [options]  <deltafile>
+.br
+.B dnadiff
+.RI [options]  <reference>  <query>
+or
+.RI [options]  -d <delta file>
+.br
+.B exact-tandems
+.RI <file> <min-match-len>
+.br
+.B gaps
+.br
+.B mapview
+.RI [options]  <coords file>  [UTR coords]  [CDS coords]
+.br
+.B mgaps
+.RI [-d <DiagDiff>] [-f <DiagFactor>] [-l <MatchLen>] [-s <MaxSeparation>]
+.br
+.B mummer
+.RI [ options ] <reference-file> <query-files>
+.br
+.B mummerplot
+.RI [options]  <match file>
+.br
+.B nucmer
+.RI [options]  <Reference>  <Query>
+.br
+.B nucmer2xfig
+.br
+.B promer
+.RI [options]  <Reference>  <Query>
+.br
+.B repeat-match
+.RI [options]  <genome-file>
+.br
+.B run-mummer1
+.RI <fasta reference> <fasta query> <prefix> [-r]
+.br
+.B run-mummer3
+.RI <fasta reference> <multi-fasta query> <prefix>
+.br
+.B show-aligns
+.RI [options]  <deltafile>  <ref ID>  <qry ID>
+.PP
+Input is the .delta output of either the "nucmer" or the
+"promer" program passed on the command line.
+.PP
+Output is to stdout, and consists of all the alignments between the
+query and reference sequences identified on the command line.
+.PP
+NOTE: No sorting is done by default, therefore the alignments
+will be ordered as found in the <deltafile> input.
+.br
+.B show-coords
+.RI [options]  <deltafile>
+.br
+.B show-snps
+.RI [options]  <deltafile>
+.br
+.B show-tiling
+.RI [options]  <deltafile>
+
+.br
+.SH DESCRIPTION
+
+.SH OPTIONS
+All tools (exept for gaps) obey to the -h, --help, -V and --version options
+as one would expect. This help is excellent and makes these man pages basically obsolete.
+.br
+.B combineMUMs
+Combines MUMs in <GapsFile> by extending matches off
+ends and between MUMs.  <RefSequence> is a fasta file
+of the reference sequence.  <MatchSequences> is a
+multi-fasta file of the sequences matched against the
+reference
+.PP
+  -D      Only output to stdout the difference positions
+          and characters
+  -n      Allow matches only between nucleotides, i.e., ACGTs
+  -N num  Break matches at <num> or more consecutive non-ACGTs 
+  -q tag  Used to label query match
+  -r tag  Used to label reference match
+  -S      Output all differences in strings
+  -t      Label query matches with query fasta header
+  -v num  Set verbose level for extra output
+  -W file Reset the default output filename witherrors.gaps
+  -x      Don't output .cover files
+  -e      Set error-rate cutoff to e (e.g. 0.02 is two percent)
+.br
+.B dnadiff
+Run comparative analysis of two sequence sets using nucmer and its
+associated utilities with recommended parameters. See MUMmer
+documentation for a more detailed description of the
+output. Produces the following output files:
+.PP       
+    .report  - Summary of alignments, differences and SNPs
+    .delta   - Standard nucmer alignment output
+    .1delta  - 1-to-1 alignment from delta-filter -1
+    .mdelta  - M-to-M alignment from delta-filter -m
+    .1coords - 1-to-1 coordinates from show-coords -THrcl .1delta
+    .mcoords - M-to-M coordinates from show-coords -THrcl .mdelta
+    .snps    - SNPs from show-snps -rlTHC .1delta
+    .rdiff   - Classified ref breakpoints from show-diff -rH .mdelta
+    .qdiff   - Classified qry breakpoints from show-diff -qH .mdelta
+    .unref   - Unaligned reference IDs and lengths (if applicable)
+    .unqry   - Unaligned query IDs and lengths (if applicable)
+.PP
+MANDATORY:
+    reference       Set the input reference multi-FASTA filename
+    query           Set the input query multi-FASTA filename
+      or
+    delta file      Unfiltered .delta alignment file from nucmer
+.PP
+OPTIONS:
+    -d|delta        Provide precomputed delta file for analysis
+    -h
+    --help          Display help information and exit
+    -p|prefix       Set the prefix of the output files (default "out")
+    -V
+    --version       Display the version information and exit
+
+.br
+.B delta-filter
+  -e float    For switches -g -r -q, keep repeats within e percent
+              of the best LIS score [0, 100], no repeats by default
+  -g          Global alignment using length*identity weighted LIS.
+              For every reference-query pair, leave only the aligns
+              which form the longest mutually consistent set
+  -h          Display help information
+  -i float    Set the minimum alignment identity [0, 100], default 0
+  -l int      Set the minimum alignment length, default 0
+  -q          Query alignment using length*identity weighted LIS.
+              For each query, leave only the aligns which form the
+              longest consistent set for the query
+  -r          Reference alignment using length*identity weighted LIS.
+              For each reference, leave only the aligns which form
+              the longest consistent set for the reference
+  -u float    Set the minimum alignment uniqueness, i.e. percent of
+              the alignment matching to unique reference AND query
+              sequence [0, 100], default 0
+  -o float    Set the maximum alignment overlap for -r and -q options
+              as a percent of the alignment length [0, 100], default 100
+.PP 
+  Reads a delta alignment file from either nucmer or promer and
+filters the alignments based on the command-line switches, leaving
+only the desired alignments which are output to stdout in the same
+delta format as the input. For multiple switches, order of operations
+is as follows: -i -l -u -q -r -g. If an alignment is excluded by a
+preceding operation, it will be ignored by the succeeding operations
+.PP
+  An important distinction between the -g option and the -r -q
+options is that -g requires the alignments to be mutually consistent
+in their order, while the -r -q options are not required to be
+mutually consistent and therefore tolerate translocations,
+inversions, etc. Thus, -r provides a one-to-many, -q a many-to-one,
+-r -q a one-to-one local mapping, and -g a one-to-one global mapping
+of reference and query bases respectively.
+.br
+.B mapview
+.br
+  -h
+.br
+  --help   Display help information and exit
+.br
+  -m|mag   Set the magnification at which the figure is rendered,
+           this is an option for fig2dev which is used to generate
+           the PDF and PS files (default 1.0)
+.br
+  -n|num   Set the number of output files used to partition the
+           output, this is to avoid generating files that are too
+           large to display (default 10)
+.br
+  -p|prefix  Set the output file prefix
+           (default "PROMER_graph or NUCMER_graph")
+.br
+  -v
+  --verbose  Verbose logging of the processed files
+.br
+  -V
+  --version  Display the version information and exit
+.br
+  -x1 coord  Set the lower coordinate bound of the display
+.br
+  -x2 coord  Set the upper coordinate bound of the display
+.br
+  -g|ref     If the input file is provided by 'mgaps', set the
+             reference sequence ID (as it appears in the first column
+             of the UTR/CDS coords file)
+.br
+  -I         Display the name of query sequences
+.br
+  -Ir        Display the name of reference genes
+.br
+.B mummer
+Find and output (to stdout) the positions and length of all
+sufficiently long maximal matches of a substring in
+<query-file> and <reference-file>
+
+  -mum           compute maximal matches that are unique in both sequences
+  -mumcand       same as -mumreference
+  -mumreference  compute maximal matches that are unique in
+ 		 the reference-sequence but not necessarily
+		 in the query-sequence (default)
+  -maxmatch      compute all maximal matches regardless of their uniqueness
+  -n             match only the characters a, c, g, or t
+                 they can be in upper or in lower case
+  -l             set the minimum length of a match
+                 if not set, the default value is 20
+  -b             compute forward and reverse complement matches
+  -r             only compute reverse complement matches
+  -s             show the matching substrings
+  -c             report the query-position of a reverse complement match
+                 relative to the original query sequence
+  -F             force 4 column output format regardless of the number of
+                 reference sequence inputs
+  -L             show the length of the query sequences on the header line
+.br
+.B nuncmer
+    nucmer generates nucleotide alignments between two mutli-FASTA input
+    files. Two output files are generated. The .cluster output file lists
+    clusters of matches between each sequence. The .delta file lists the
+    distance between insertions and deletions that produce maximal scoring
+    alignments between each sequence.
+
+.I MANDATORY:
+    Reference     Set the input reference multi-FASTA filename
+    Query         Set the input query multi-FASTA filename
+
+  --mum           Use anchor matches that are unique in both the reference
+                  and query
+  --mumcand       Same as --mumreference
+  --mumreference  Use anchor matches that are unique in in the reference
+                  but not necessarily unique in the query (default behavior)
+  --maxmatch      Use all anchor matches regardless of their uniqueness
+
+  -b|breaklen     Set the distance an alignment extension will attempt to
+                  extend poor scoring regions before giving up (default 200)
+  -c|mincluster   Sets the minimum length of a cluster of matches (default 65)
+  --[no]delta     Toggle the creation of the delta file (default --delta)
+  --depend        Print the dependency information and exit
+  -d|diagfactor   Set the clustering diagonal difference separation factor
+                  (default 0.12)
+  --[no]extend    Toggle the cluster extension step (default --extend)
+  -f
+  --forward       Use only the forward strand of the Query sequences
+  -g|maxgap       Set the maximum gap between two adjacent matches in a
+                  cluster (default 90)
+  -h
+  --help          Display help information and exit
+  -l|minmatch     Set the minimum length of a single match (default 20)
+  -o
+  --coords        Automatically generate the original NUCmer1.1 coords
+                  output file using the 'show-coords' program
+  --[no]optimize  Toggle alignment score optimization, i.e. if an alignment
+                  extension reaches the end of a sequence, it will backtrack
+                  to optimize the alignment score instead of terminating the
+                  alignment at the end of the sequence (default --optimize)
+  -p|prefix       Set the prefix of the output files (default "out")
+  -r
+  --reverse       Use only the reverse complement of the Query sequences
+  --[no]simplify  Simplify alignments by removing shadowed clusters. Turn
+                  this option off if aligning a sequence to itself to look
+                  for repeats (default --simplify)
+    
+.br
+.B promer
+    promer generates amino acid alignments between two mutli-FASTA DNA input
+    files. Two output files are generated. The .cluster output file lists
+    clusters of matches between each sequence. The .delta file lists the
+    distance between insertions and deletions that produce maximal scoring
+    alignments between each sequence. The DNA input is translated into all 6
+    reading frames in order to generate the output, but the output coordinates
+    reference the original DNA input.
+
+.I MANDATORY:
+    Reference     Set the input reference multi-FASTA DNA file
+    Query         Set the input query multi-FASTA DNA file
+
+  --mum           Use anchor matches that are unique in both the reference
+                  and query
+  --mumcand       Same as --mumreference
+  --mumreference  Use anchor matches that are unique in in the reference
+                  but not necessarily unique in the query (default behavior)
+  --maxmatch      Use all anchor matches regardless of their uniqueness
+
+  -b|breaklen     Set the distance an alignment extension will attempt to
+                  extend poor scoring regions before giving up, measured in
+                  amino acids (default 60)
+  -c|mincluster   Sets the minimum length of a cluster of matches, measured in
+                  amino acids (default 20)
+  --[no]delta     Toggle the creation of the delta file (default --delta)
+  --depend        Print the dependency information and exit
+  -d|diagfactor   Set the clustering diagonal difference separation factor
+                  (default .11)
+  --[no]extend    Toggle the cluster extension step (default --extend)
+  -g|maxgap       Set the maximum gap between two adjacent matches in a
+                  cluster, measured in amino acids (default 30)
+  -l|minmatch     Set the minimum length of a single match, measured in amino
+                  acids (default 6)
+  -m|masklen      Set the maximum bookend masking lenth, measured in amino
+                  acids (default 8)
+  -o
+  --coords        Automatically generate the original PROmer1.1 ".coords"
+                  output file using the "show-coords" program
+  --[no]optimize  Toggle alignment score optimization, i.e. if an alignment
+                  extension reaches the end of a sequence, it will backtrack
+                  to optimize the alignment score instead of terminating the
+                  alignment at the end of the sequence (default --optimize)
+
+  -p|prefix       Set the prefix of the output files (default "out")
+  -x|matrix       Set the alignment matrix number to 1 [BLOSUM 45],
+                  2 [BLOSUM 62] or 3 [BLOSUM 80] (default 2)
+.br
+.B repeat-match
+Find all maximal exact matches in <genome-file>
+  -E    Use exhaustive (slow) search to find matches
+  -f    Forward strand only, don't use reverse complement
+  -n #  Set minimum exact match length to #
+  -t    Only output tandem repeats
+  -V #  Set level of verbose (debugging) printing to #
+.br
+.B show-aligns
+  -h      Display help information
+  -q      Sort alignments by the query start coordinate
+  -r      Sort alignments by the reference start coordinate
+  -w int  Set the screen width - default is 60
+  -x int  Set the matrix type - default is 2 (BLOSUM 62),
+          other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
+          note: only has effect on amino acid alignments
+.br
+.B show-coords
+  -b          Merges overlapping alignments regardless of match dir
+              or frame and does not display any idenitity information.
+  -B          Switch output to btab format
+  -c          Include percent coverage information in the output
+  -d          Display the alignment direction in the additional
+              FRM columns (default for promer)
+  -g          Deprecated option. Please use 'delta-filter' instead
+  -h          Display help information
+  -H          Do not print the output header
+  -I float    Set minimum percent identity to display
+  -k          Knockout (do not display) alignments that overlap
+              another alignment in a different frame by more than 50%
+              of their length, AND have a smaller percent similarity
+              or are less than 75% of the size of the other alignment
+              (promer only)
+  -l          Include the sequence length information in the output
+  -L long     Set minimum alignment length to display
+  -o          Annotate maximal alignments between two sequences, i.e.
+              overlaps between reference and query sequences
+  -q          Sort output lines by query IDs and coordinates
+  -r          Sort output lines by reference IDs and coordinates
+  -T          Switch output to tab-delimited format
+
+  Input is the .delta output of either the "nucmer" or the
+"promer" program passed on the command line.
+.PP
+  Output is to stdout, and consists of a list of coordinates,
+percent identity, and other useful information regarding the
+alignment data contained in the .delta file used as input.
+.PP
+  NOTE: No sorting is done by default, therefore the alignments
+will be ordered as found in the <deltafile> input.
+.br
+.B show-snps
+  -C            Do not report SNPs from alignments with an ambiguous
+                mapping, i.e. only report SNPs where the [R] and [Q]
+                columns equal 0 and do not output these columns
+  -h            Display help information
+  -H            Do not print the output header
+  -I            Do not report indels
+  -l            Include sequence length information in the output
+  -q            Sort output lines by query IDs and SNP positions
+  -r            Sort output lines by reference IDs and SNP positions
+  -S            Specify which alignments to report by passing
+                'show-coords' lines to stdin
+  -T            Switch to tab-delimited format
+  -x int        Include x characters of surrounding SNP context in the
+                output, default 0
+  
+  Input is the .delta output of either the nucmer or promer program
+passed on the command line.
+.PP
+  Output is to stdout, and consists of a list of SNPs (or amino acid
+substitutions for promer) with positions and other useful info.
+Output will be sorted with -r by default and the [BUFF] column will
+always refer to the sequence whose positions have been sorted. This
+value specifies the distance from this SNP to the nearest mismatch
+(end of alignment, indel, SNP, etc) in the same alignment, while the
+[DIST] column specifies the distance from this SNP to the nearest
+sequence end. SNPs for which the [R] and [Q] columns are greater than
+0 should be evaluated with caution, as these columns specify the
+number of other alignments which overlap this position. Use -C to
+assure SNPs are only reported from unique alignment regions.
+
+.B show-tiling
+  -a          Describe the tiling path by printing the tab-delimited
+              alignment region coordinates to stdout
+  -c          Assume the reference sequences are circular, and allow
+              tiled contigs to span the origin
+  -g int      Set maximum gap between clustered alignments [-1, INT_MAX]
+              A value of -1 will represent infinity
+              (nucmer default = 1000)
+              (promer default = -1)
+  -i float    Set minimum percent identity to tile [0.0, 100.0]
+              (nucmer default = 90.0)
+              (promer default = 55.0)
+  -l int      Set minimum length contig to report [-1, INT_MAX]
+              A value of -1 will represent infinity
+              (common default = 1)
+  -p file     Output a pseudo molecule of the query contigs to 'file'
+  -R          Deal with repetitive contigs by randomly placing them
+              in one of their copy locations (implies -V 0)
+  -t file     Output a TIGR style contig list of each query sequence
+              that sufficiently matches the reference (non-circular)
+  -u file     Output the tab-delimited alignment region coordinates
+              of the unusable contigs to 'file'
+  -v float    Set minimum contig coverage to tile [0.0, 100.0]
+              (nucmer default = 95.0) sum of individual alignments
+              (promer default = 50.0) extent of syntenic region
+  -V float    Set minimum contig coverage difference [0.0, 100.0]
+              i.e. the difference needed to determine one alignment
+              is 'better' than another alignment
+              (nucmer default = 10.0) sum of individual alignments
+              (promer default = 30.0) extent of syntenic region
+  -x          Describe the tiling path by printing the XML contig
+              linking information to stdout
+
+  Input is the .delta output of the nucmer program, run on very
+similar sequence data, or the .delta output of the promer program,
+run on divergent sequence data.
+.PP
+  Output is to stdout, and consists of the predicted location of
+each aligning query contig as mapped to the reference sequences.
+These coordinates reference the extent of the entire query contig,
+even when only a certain percentage of the contig was actually
+aligned (unless the -a option is used). Columns are, start in ref,
+end in ref, distance to next contig, length of this contig, alignment
+coverage, identity, orientation, and ID respectively.
+
+.SH SEE ALSO
+.BR http://mummer.sourceforge.net/ 
+.br
+.PP
+Open source MUMmer 3.0 is described in
+.br
+.I "Versatile and open software for comparing large genomes."
+S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg, Genome Biology (2004), 5:R12.
+.SH AUTHOR
+mummer was written by S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg.

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.README.Debian
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.README.Debian	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.README.Debian	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,7 @@
+mummer for Debian
+-----------------
+
+The program annotate was renamed to mummer-annotate to avoid
+name space pollution with libgd-tools.
+
+ -- Andreas Tille <tille at debian.org>, Mon, 7 May 2007 14:46:27 +0200

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.desktop
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.desktop	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.desktop	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,10 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Exec=mummer
+Name=mummer
+GenericName=Efficient sequence alignment of full genomes
+GenericName[en]=Efficient sequence alignment of full genomes
+Type=Application
+Categories=Education;Science;Biology;

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.dirs
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.dirs	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.dirs	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,5 @@
+usr/sbin
+usr/lib/mummer/bin
+usr/lib/mummer/lib
+usr/lib/mummer/scripts
+

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.docs
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.docs	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.docs	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,2 @@
+README
+ACKNOWLEDGEMENTS

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.install
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.install	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.install	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,3 @@
+bin/*                 usr/bin
+aux_bin               usr/lib/mummer
+scripts/Foundation.pm usr/share/perl5

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.links
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.links	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.links	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,19 @@
+usr/share/man/man1/mummer.1 usr/share/man/man1/mummer-annotate.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/combineMUMs.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/dnadiff.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/delta-filter.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/exact-tandems.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/gaps.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/mapview.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/mgaps.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/mummerplot.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/nucmer.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/nucmer2xfig.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/promer.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/repeat-match.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/run-mummer1.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/run-mummer3.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/show-aligns.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/show-coords.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/show-snps.1
+usr/share/man/man1/mummer.1 usr/share/man/man1/show-tiling.1

Added: trunk/packages/mummer/tags/3.20-2/debian/mummer.manpages
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/mummer.manpages	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/mummer.manpages	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1 @@
+debian/mummer.1

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_docs.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_docs.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_docs.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,11 @@
+diff -urbN docs.orig/Makefile docs/Makefile
+--- docs.orig/Makefile	2005-05-20 22:28:54.000000000 +0200
++++ docs/Makefile	2007-03-30 14:53:07.000000000 +0200
+@@ -1,6 +1,6 @@
+ LATEX=pdflatex
+ 
+-maxmat3man.dvi:maxmat3man.tex
++maxmat3man.pdf:maxmat3man.tex
+ 	${LATEX} maxmat3man
+ 	${LATEX} maxmat3man
+ 

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_kurtz.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_kurtz.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_kurtz.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,98 @@
+diff -urbN src/kurtz.orig/Makefile src/kurtz/Makefile
+--- src/kurtz.orig/Makefile	2007-07-13 19:06:58.000000000 +0200
++++ src/kurtz/Makefile	2007-11-07 21:47:03.000000000 +0100
+@@ -1,20 +1,21 @@
+ all:
+-	cd libbasedir; $(MAKE) all
+-	cd streesrc; $(MAKE) all
+-	cd mm3src; $(MAKE) all
++	$(MAKE) -C libbasedir all
++	$(MAKE) -C streesrc all
++	$(MAKE) BIN_DIR="../../../bin" -C mm3src all
+ 
+ clean:
+ 	rm -f *~
+-	cd libbasedir; $(MAKE) clean
+-	cd streesrc; $(MAKE) clean
+-	cd mm3src; $(MAKE) clean
++	$(MAKE) -C libbasedir clean
++	$(MAKE) -C streesrc clean
++	$(MAKE) -C mm3src clean
++	rm -rf bin
+ 
+ mummer:
+-	cd libbasedir; $(MAKE) libbase.a
+-	cd streesrc; $(MAKE) libstree.a
+-	cd mm3src; $(MAKE) mummer
++	$(MAKE) -C libbasedir libbase.a
++	$(MAKE) -C streesrc libstree.a
++	$(MAKE) BIN_DIR="../../../bin" -C mm3src mummer
+ 
+ splintall:
+-	cd libbasedir; ${MAKE} splintall
+-	cd streesrc; ${MAKE} splintall
+-	cd mm3src; ${MAKE} splintall
++	${MAKE} -C libbasedir splintall
++	${MAKE} -C streesrc splintall
++	${MAKE} -C mm3src splintall
+diff -urbN src/kurtz.orig/mm3src/Makefile src/kurtz/mm3src/Makefile
+--- src/kurtz.orig/mm3src/Makefile	2007-07-13 19:06:58.000000000 +0200
++++ src/kurtz/mm3src/Makefile	2007-11-07 21:47:03.000000000 +0100
+@@ -3,12 +3,10 @@
+ 
+ ##include ../Makedef
+ 
+-ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
++ifndef INSTALL_BIN_DIR
++INSTALL_BIN_DIR=../../bin
+ endif
+ 
+-VPATH := $(BIN_DIR)
+-
+ ALL := maxmat3.x maxmat3.dbg.x
+ 
+ LIBBASEDIR=../libbasedir
+@@ -26,13 +24,13 @@
+ LIBSTREE=$(LIBSTREEDIR)/libstree.a
+ LIBSTREEDBG=$(LIBSTREEDIR)/libstree.dbg.a
+ 
+-MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o\
++MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o \
+             findmumcand.o findmaxmat.o procmaxmat.o
+ 
+-MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o\
++MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o \
+                findmumcand.dbg.o findmaxmat.dbg.o procmaxmat.dbg.o
+ 
+-SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint\
++SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint \
+           findmumcand.splint findmaxmat.splint procmaxmat.splint
+ 
+ .SUFFIXES: .dbg.o
+@@ -41,21 +39,21 @@
+ 
+ mummer: $(MUM3OBJECTS) $(LIBSTREE)
+ 	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+-	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++	-o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+ 
+ maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
+ 	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+-	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++	-o $(INSTALL_BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+ 
+ maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
+ 	$(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
+-	-lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++	-lm -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+ 
+ include Filegoals.mf
+ 
+ .PHONY:clean
+ clean:splintclean
+ 	rm -f *.[ox] shit[123] *~
+-	cd $(BIN_DIR); rm -f $(ALL) mummer
++	rm -f $(BIN_DIR)/mummer* 
+ 
+ include Dependencies.mf

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_tigr.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_tigr.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/01sm_src_tigr.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,103 @@
+diff -urbN src/tigr.orig/annotate.cc src/tigr/annotate.cc
+--- src/tigr.orig/annotate.cc	2007-07-13 19:06:58.000000000 +0200
++++ src/tigr/annotate.cc	2007-11-07 21:47:03.000000000 +0100
+@@ -10,6 +10,7 @@
+ */
+ 
+ #include "tigrinc.hh"
++#include <assert.h>
+ 
+ #define  FIELD_LEN  20
+ #define  MAX_ALIGN  10000
+@@ -138,19 +139,19 @@
+ //  Print the alignment between strings  A [1 .. M]  and  B [1 .. N] .
+ 
+   {
+-   static int  D [MAX_ALIGN] [MAX_ALIGN];
+-   static char  Op [MAX_ALIGN] [MAX_ALIGN];
+-   static char  Show_A [2 * MAX_ALIGN];
+-   static char  Show_B [2 * MAX_ALIGN];
++   int  **D,  *D_buf;
++   char **Op, *Op_buf;
++   char  *Show_A;
++   char  *Show_B;
+    int  Errors, Tmp;
+    long int  i, j, Ct;
+ 
+-   if  (M >= MAX_ALIGN || N >= MAX_ALIGN)
+-       {
+-        printf ("\n   *** Too long ***\n\n");
+-        fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
+-        return;
+-       }
++   assert ( D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
++   D  = &D_buf ;
++   assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
++   Op = &Op_buf ;
++   assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
++   assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
+ 
+    D [0] [0] = 0;
+    Op [0] [0] = 'a';
+@@ -229,5 +230,10 @@
+       putchar ('\n');
+       Ct -= WIDTH;
+      }  while  (Ct > 0);
++
++   free ( D_buf ) ;
++   free ( Op_buf ) ;
++   free ( Show_A ) ;
++   free ( Show_B ) ;
+    return;
+   }
+diff -urbN src/tigr.orig/Makefile src/tigr/Makefile
+--- src/tigr.orig/Makefile	2007-07-13 19:06:58.000000000 +0200
++++ src/tigr/Makefile	2007-11-07 21:47:03.000000000 +0100
+@@ -2,23 +2,20 @@
+ # BIN_DIR AUX_BIN_DIR CXX CC CPPFLAGS LDFLAGS
+ 
+ ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
++BIN_DIR := ../../bin
+ endif
+ ifndef AUX_BIN_DIR
+-AUX_BIN_DIR := $(CURDIR)
++AUX_BIN_DIR := ../../aux_bin
+ endif
+ 
+ OBJ_RULE = $(CXX) $(CPPFLAGS) $< -c -o $@
+-BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@; \
+-           chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+-           chmod 755 $(AUX_BIN_DIR)/$@
++BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
++AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@ && chmod 755 $(AUX_BIN_DIR)/$@
+ VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+ 
+ ALL := annotate combineMUMs delta-filter gaps mgaps \
+      postnuc postpro prenuc prepro repeat-match \
+-     show-aligns show-coords show-tiling show-snps \
+-     show-diff
++     show-aligns show-coords show-tiling show-snps
+ 
+ 
+ #-- PHONY rules --#
+@@ -30,10 +27,8 @@
+ 
+ clean:
+ 	rm -f *.o *~
+-	cd $(BIN_DIR); rm -f $(ALL)
+-	cd $(AUX_BIN_DIR); rm -f $(ALL)
+-
+-
++	( cd $(BIN_DIR) && rm -f $(ALL) )
++	( cd $(AUX_BIN_DIR) && rm -f $(ALL) )
+ 
+ 
+ #-- not so PHONY rules --#
+@@ -92,5 +87,3 @@
+ show-snps: show-snps.cc tigrinc.o translate.o delta.o
+ 	$(BIN_RULE)
+ 
+-show-diff: show-diff.cc tigrinc.o delta.o
+-	$(BIN_RULE)

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/02at_Makefile.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/02at_Makefile.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/02at_Makefile.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,38 @@
+--- Makefile.orig	2006-06-29 19:35:08.000000000 +0200
++++ Makefile	2007-04-13 13:49:11.000000000 +0200
+@@ -27,7 +27,7 @@
+ 
+ 
+ TOP_DIR     := $(CURDIR)
+-BIN_DIR     := $(TOP_DIR)
++BIN_DIR     := $(TOP_DIR)/bin
+ AUX_BIN_DIR := $(TOP_DIR)/aux_bin
+ 
+ DOC_DIR       := $(TOP_DIR)/docs
+@@ -93,6 +93,7 @@
+ 	cd $(TIGR_SRC_DIR); $(MAKE) clean
+ 	cd $(SCRIPT_DIR); $(MAKE) clean
+ 	cd $(DOC_DIR); $(MAKE) clean
++	-if [ $(BIN_DIR) != $(TOP_DIR) ] ; then rmdir $(BIN_DIR) ; fi
+ 
+ 
+ dist: DISTDIR = MUMmer$(VERSION)
+@@ -113,6 +114,7 @@
+ 
+ 
+ kurtz:
++	mkdir -p $(BIN_DIR)
+ 	cd $(KURTZ_SRC_DIR); $(MAKE) mummer
+ 
+ 
+@@ -124,6 +126,10 @@
+ 	cd $(TIGR_SRC_DIR); $(MAKE) all
+ 
+ 
++doc:
++	cd $(DOC_DIR); $(MAKE)
++
++
+ uninstall: clean
+ 
+ 

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/02at_docs_web.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/02at_docs_web.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/02at_docs_web.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,29 @@
+--- docs/web/index.html.orig	2006-06-29 19:35:07.000000000 +0200
++++ docs/web/index.html	2007-05-07 14:07:52.000000000 +0200
+@@ -125,7 +125,7 @@
+   <h3><em><font color="#CC0000"> Applications </font></em></h3>
+   <p>MUMmer 1.0 was used to detect numerous large-scale inversions in bacterial 
+     genomes, leading to a new model of chromosome inversions, reported in this 
+-    <a href=XFiles.pdf>2000 <em>Genome Biology</em> paper</a>. It was also used 
++    <a href="http://mummer.sourceforge.net/XFiles.pdf">2000 <em>Genome Biology</em> paper</a>. It was also used 
+     to discover evidence for a recent whole-genome duplication in <em>Arabidopsis 
+     thaliana</em>, reported in "Analysis of the genome sequence of the flowering 
+     plant <em>Arabidopsis thaliana</em>." The Arabidopsis Genome Initiative, <em>Nature</em> 
+@@ -177,14 +177,14 @@
+   <h3><a href="manual">MUMmer3.0 user manual</a></h3>
+   <h3><a href="examples">MUMmer3.0 examples</a></h3>
+   <p>Open source MUMmer 3.0 is described in "<a
+-        href=MUMmer3.pdf>Versatile and open software for comparing large genomes</a>." 
++        href="http://mummer.sourceforge.net/MUMmer3.pdf">Versatile and open software for comparing large genomes</a>." 
+     S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, 
+     and S.L. Salzberg, <em>Genome Biology</em> (2004), 5:R12.</p>
+-  <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href=MUMmer2.pdf>Fast 
++  <p>MUMmer 2.1, NUCmer, and PROmer are described in "<a href="http://mummer.sourceforge.net/MUMmer2.pdf">Fast 
+     Algorithms for Large-scale Genome Alignment and Comparision</a>." A.L. Delcher, 
+     A. Phillippy, J. Carlton, and S.L. Salzberg, <em>Nucleic Acids Research</em> 
+     (2002), Vol. 30, No. 11 2478-2483.</p>
+-  <p>MUMmer 1.0 is described in "<a href=MUMmer.pdf>Alignment of Whole Genomes</a>." 
++  <p>MUMmer 1.0 is described in "<a href="http://mummer.sourceforge.net/MUMmer.pdf">Alignment of Whole Genomes</a>." 
+     A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. 
+     Salzberg, <em>Nucleic Acids Research</em>, 27:11 (1999), 2369-2376.</p>
+   <p>Space efficent suffix trees are described in "<a href=http://www.zbh.uni-hamburg.de/staff/kurtz/papers/Kur1999.pdf>Reducing 

Added: trunk/packages/mummer/tags/3.20-2/debian/patches/02at_scripts.diff
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/patches/02at_scripts.diff	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/patches/02at_scripts.diff	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,241 @@
+diff -ubrN MUMmer3.20/scripts.orig/exact-tandems.sh MUMmer3.20/scripts/exact-tandems.sh
+--- MUMmer3.20/scripts.orig/exact-tandems.sh	1970-01-01 01:00:00.000000000 +0100
++++ MUMmer3.20/scripts/exact-tandems.sh	2007-11-12 13:12:31.000000000 +0100
+@@ -0,0 +1,34 @@
++#!/bin/sh -e
++#
++# Find exact tandem repeats in specified file involving an
++# exact duplicate of at least the specified length
++
++usage () {
++    echo "Usage: `basename $0` <file> <min-match-len>"
++    return 67 # EX_USAGE
++}
++
++if [ $# -ne 2 ] ; then
++    echo "You provided $# arguments instead of 2."
++    usage
++fi
++
++filename="$1"
++matchlen="$2"
++
++bindir=__BIN_DIR
++scriptdir=__SCRIPT_DIR
++
++if  [ ! -e "$filename"  ] ; then
++    echo "File $filename does not exist."
++    usage
++fi
++
++echo "Finding matches"
++$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.tmp.matches
++# This is default behavior when shell started with -e
++# if  ($status != 0)  exit -1
++
++echo "Tandem repeats"
++sort -k1n -k2n $$.tmp.matches | awk -f $scriptdir/tandem-repeat.awk
++rm -f $$.tmp.matches
+diff -ubrN MUMmer3.20/scripts.orig/Makefile MUMmer3.20/scripts/Makefile
+--- MUMmer3.20/scripts.orig/Makefile	2007-07-13 19:06:57.000000000 +0200
++++ MUMmer3.20/scripts/Makefile	2007-11-12 13:15:01.000000000 +0100
+@@ -7,9 +7,18 @@
+ ifndef AUX_BIN_DIR
+ AUX_BIN_DIR := $(CURDIR)
+ endif
++ifndef INSTALL_AUX_BIN_DIR
++INSTALL_AUX_BIN_DIR := $(AUX_BIN_DIR)
++endif
+ ifndef SCRIPT_DIR
+ SCRIPT_DIR := $(CURDIR)
+ endif
++ifndef INSTALL_BIN_DIR
++INSTALL_BIN_DIR := $(BIN_DIR)
++endif
++ifndef INSTALL_SCRIPT_DIR
++INSTAL_SCRIPT_DIR := $(SCRIPT_DIR)
++endif
+ 
+ SCRIPT_DIR := $(CURDIR)
+ SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
+@@ -29,68 +38,24 @@
+ 
+ clean:
+ 	rm -f *~
+-	cd $(BIN_DIR); rm -f $(ALL)
+-
+-
++	( cd $(BIN_DIR); rm -f $(ALL) )
+ 
++#-- replace variables by real path names --#
+ 
+-#-- not so PHONY rules --#
+-exact-tandems: exact-tandems.csh
+-	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-		exact-tandems.csh > $(BIN_DIR)/exact-tandems
+-	chmod 755 $(BIN_DIR)/exact-tandems
++%:
++	$(SED)  -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
++		-e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
++		-e 's?__PERL_PATH?$(PERL)?g' \
++		-e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
++		$< > $(BIN_DIR)/$@
++	chmod 755 $(BIN_DIR)/$@
+ 
++exact-tandems: exact-tandems.sh
+ mapview: mapview.pl
+-	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                mapview.pl > $(BIN_DIR)/mapview
+-	chmod 755 $(BIN_DIR)/mapview
+-
+ mummerplot: mummerplot.pl Foundation.pm
+-	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-                mummerplot.pl > $(BIN_DIR)/mummerplot
+-	chmod 755 $(BIN_DIR)/mummerplot
+-
+ dnadiff: dnadiff.pl Foundation.pm
+-	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
+-               -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-               -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-                 dnadiff.pl > $(BIN_DIR)/dnadiff
+-	chmod 755 $(BIN_DIR)/dnadiff
+-
+ nucmer: nucmer.pl Foundation.pm
+-	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-                 nucmer.pl > $(BIN_DIR)/nucmer
+-	chmod 755 $(BIN_DIR)/nucmer
+-
+ promer: promer.pl Foundation.pm
+-	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+-                -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
+-                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-                promer.pl > $(BIN_DIR)/promer
+-	chmod 755 $(BIN_DIR)/promer
+-
+-run-mummer1: run-mummer1.csh
+-	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-		run-mummer1.csh > $(BIN_DIR)/run-mummer1
+-	chmod 755 $(BIN_DIR)/run-mummer1
+-
+-run-mummer3: run-mummer3.csh
+-	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
+-		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
+-		run-mummer3.csh > $(BIN_DIR)/run-mummer3
+-	chmod 755 $(BIN_DIR)/run-mummer3
+-
++run-mummer1:   run-mummer1.sh
++run-mummer3:   run-mummer3.sh
+ nucmer2xfig: nucmer2xfig.pl
+-	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
+-		nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
+-	chmod 755 $(BIN_DIR)/nucmer2xfig
+diff -ubrN MUMmer3.20/scripts.orig/run-mummer1.sh MUMmer3.20/scripts/run-mummer1.sh
+--- MUMmer3.20/scripts.orig/run-mummer1.sh	1970-01-01 01:00:00.000000000 +0100
++++ MUMmer3.20/scripts/run-mummer1.sh	2007-11-12 13:12:31.000000000 +0100
+@@ -0,0 +1,45 @@
++#!/bin/sh -e
++#
++# **SEVERELY** antiquated script for running the mummer 1 suite
++# -r option reverse complements the query sequence, coordinates of the reverse
++# matches will be relative to the reversed sequence
++#
++
++usage () {
++    echo "Usage: `basename $0` <fasta reference> <fasta query> <prefix> [-r]"
++    return 67 # EX_USAGE
++}
++
++if [ $# -ne 3 -a $# -ne 4 ] ; then
++    echo "You provided $# arguments."
++    usage
++fi
++
++ref="$1"
++qry="$2"
++pfx="$3"
++rev="$4"
++
++bindir=__BIN_DIR
++
++if  [ ! -e "$ref"  ] ; then
++    echo "File for fasta reference $ref does not exist."
++    usage
++fi
++
++if  [ ! -e "$qry"  ] ; then
++    echo "File for fasta query $qry does not exist."
++    usage
++fi
++
++if [ "$pfx" = "" ] ; then
++    usage
++fi
++
++echo "Find MUMs"
++$bindir/mummer -mum -l 20 "$rev" "$ref" "$qry" | tail +2 > "$pfx".out
++echo "Determine gaps"
++$bindir/gaps "$ref" "$rev" < "$pfx".out > "$pfx".gaps
++echo "Align gaps"
++$bindir/mummer-annotate "$pfx".gaps "$qry" > "$pfx".align
++mv witherrors.gaps "$pfx".errorsgaps
+diff -ubrN MUMmer3.20/scripts.orig/run-mummer3.sh MUMmer3.20/scripts/run-mummer3.sh
+--- MUMmer3.20/scripts.orig/run-mummer3.sh	1970-01-01 01:00:00.000000000 +0100
++++ MUMmer3.20/scripts/run-mummer3.sh	2007-11-12 13:12:31.000000000 +0100
+@@ -0,0 +1,47 @@
++#!/bin/sh -e
++#
++# for running the basic mummer 3 suite, should use nucmer instead when possible
++# to avoid the confusing reverse coordinate system of the raw programs.
++#
++# NOTE:  be warned that all reverse matches will then
++# be relative to the reverse complement of the query sequence.
++#
++# Edit this script as necessary to alter the matching and clustering values
++#
++
++usage () {
++    echo "Usage: `basename $0` <fasta reference> <multi-fasta query> <prefix>"
++    return 67 # EX_USAGE
++}
++
++if [ $# -ne 3 ] ; then
++    echo "You provided $# arguments."
++    usage
++fi
++
++ref="$1"
++qry="$2"
++pfx="$3"
++
++bindir=__BIN_DIR
++
++if  [ ! -e "$ref"  ] ; then
++    echo "File for fasta reference $ref does not exist."
++    usage
++fi
++
++if  [ ! -e "$qry"  ] ; then
++    echo "File for fasta query $qry does not exist."
++    usage
++fi
++
++if [ "$pfx" = "" ] ; then
++    usage
++fi
++
++echo "Find MUMs"
++$bindir/mummer -mumreference -b -l 20 "$ref" "$qry" > "$pfx".out
++echo "Determine gaps"
++$bindir/mgaps -l 100 -f .12 -s 600 < "$pfx".out > "$pfx".gaps
++echo "Align gaps"
++$bindir/combineMUMs -x -e .10 -W "$pfx".errorsgaps "$ref" "$qry" "$pfx".gaps > "$pfx".align

Added: trunk/packages/mummer/tags/3.20-2/debian/rules
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/rules	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/rules	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,39 @@
+#!/usr/bin/make -f
+# debian/rules for mummer using cdbs
+# Andreas Tille <tille at debian.org>, GPL
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk  
+include /usr/share/cdbs/1/class/makefile.mk  
+
+# prevent compression of PDF docs
+DEB_COMPRESS_EXCLUDE := .pdf
+
+## copied from polipo package to avoid conflict whan upstream changes CFLAGS inside Makefile
+DEB_MAKE_INVOKE = $(DEB_MAKE_ENVVARS) make \
+	             INSTALL_AUX_BIN_DIR=/usr/lib/mummer/aux_bin \
+		     INSTALL_BIN_DIR=/usr/bin \
+		     INSTALL_SCRIPT_DIR=/usr/share/perl5 \
+		     -C $(DEB_BUILDDIR)
+
+configure::
+	(cd src/tigr && ln -s ../../aux_bin . )
+	make check
+
+build/mummer-doc::
+	cd doc; make
+#	$(MAKE) DESTDIR=$(CURDIR)/debian/mummer
+
+clean::
+	rm -f src/tigr/aux_bin
+	rm -rf bin
+
+# post installation
+install/mummer::
+	# install desktop file
+	# dh_desktop 
+	# prevent name space pollution because libgd-tools contains /usr/bin/annotate
+	mv bin/annotate bin/mummer-annotate
+
+get-orig-source:
+	sh debian/get-orig-source


Property changes on: trunk/packages/mummer/tags/3.20-2/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/mummer/tags/3.20-2/debian/watch
===================================================================
--- trunk/packages/mummer/tags/3.20-2/debian/watch	                        (rev 0)
+++ trunk/packages/mummer/tags/3.20-2/debian/watch	2008-01-10 15:41:04 UTC (rev 1093)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/mummer/MUMmer(.+)\.tar.gz

Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog	2008-01-10 13:10:59 UTC (rev 1092)
+++ trunk/packages/mummer/trunk/debian/changelog	2008-01-10 15:41:04 UTC (rev 1093)
@@ -1,4 +1,4 @@
-mummer (3.20-2) UNRELEASED; urgency=low
+mummer (3.20-2) unstable; urgency=low
 
   [ Charles Plessy ]
   * XS-DM-Upload-Allowed: Yes
@@ -7,8 +7,13 @@
   * Changed e-mail address in uploaders
   * Stripped long description of mummer-doc
 
- -- Andreas Tille <tille at debian.org>  Sun, 09 Dec 2007 16:25:34 +0100
+  [ Andreas Tille ]
+  * Do not install mummer.desktop because it is a command line
+    application (Fixed debian/mummer.desktop anyway)
+  * Standards-Version: 3.7.3 (no changes needed)
 
+ -- Andreas Tille <tille at debian.org>  Thu, 10 Jan 2008 12:13:24 +0100
+
 mummer (3.20-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/mummer/trunk/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control	2008-01-10 13:10:59 UTC (rev 1092)
+++ trunk/packages/mummer/trunk/debian/control	2008-01-10 15:41:04 UTC (rev 1093)
@@ -5,7 +5,7 @@
 XS-DM-Upload-Allowed: Yes
 Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>
 Build-Depends: cdbs (>= 0.4.23-1.1), patchutils (>= 0.2.25), debhelper (>= 5), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
-Standards-Version: 3.7.2
+Standards-Version: 3.7.3
 Homepage: http://mummer.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mummer

Modified: trunk/packages/mummer/trunk/debian/mummer.desktop
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.desktop	2008-01-10 13:10:59 UTC (rev 1092)
+++ trunk/packages/mummer/trunk/debian/mummer.desktop	2008-01-10 15:41:04 UTC (rev 1093)
@@ -7,4 +7,4 @@
 GenericName=Efficient sequence alignment of full genomes
 GenericName[en]=Efficient sequence alignment of full genomes
 Type=Application
-Categories=Office;Biology;Science;
+Categories=Education;Science;Biology;

Modified: trunk/packages/mummer/trunk/debian/mummer.install
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.install	2008-01-10 13:10:59 UTC (rev 1092)
+++ trunk/packages/mummer/trunk/debian/mummer.install	2008-01-10 15:41:04 UTC (rev 1093)
@@ -1,4 +1,3 @@
 bin/*                 usr/bin
 aux_bin               usr/lib/mummer
 scripts/Foundation.pm usr/share/perl5
-debian/*.desktop      usr/share/applications




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