[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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