[med-svn] r3572 - in trunk/packages/mummer/trunk/debian: . patches sh-replacement-scripts
Charles Plessy
plessy at alioth.debian.org
Mon Jun 29 10:43:16 UTC 2009
Author: plessy
Date: 2009-06-29 10:43:15 +0000 (Mon, 29 Jun 2009)
New Revision: 3572
Added:
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh
trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh
Removed:
trunk/packages/mummer/trunk/debian/patches/01sm_docs.diff
trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff
trunk/packages/mummer/trunk/debian/patches/02at_Makefile.diff
trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff
Modified:
trunk/packages/mummer/trunk/debian/changelog
trunk/packages/mummer/trunk/debian/control
trunk/packages/mummer/trunk/debian/copyright
trunk/packages/mummer/trunk/debian/mummer.desktop
trunk/packages/mummer/trunk/debian/mummer.install
trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
Log:
New upstream release and patch eradication in progress?\226?\128?\166
Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/changelog 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,17 +1,26 @@
mummer (3.21~dfsg-1) UNRELEASED; urgency=low
- TODO: refresh patches
+ PATCH ERADICATION IN PROGRESS.
+
+ OTHER TODO:
convert debian/copyright to machine-readable format
document that the following files are removed, and indicate the licence they would have had (some are freely redistributable, if not all.)
./docs/web/MUMmer.pdf
./docs/web/XFiles.pdf
./docs/web/MUMmer2.pdf
./docs/web/MUMmer3.pdf
- document and forward if necessary the patches.
forward other material such as the .desktop file.
* New upstream release (GCC compatibility fix.)
* debian/get-orig-source: rename mutilated upstream tarball.
+ * debian/control:
+ - dropped versionned dependancies when they are even satisfied in oldstable.
+ - incremented Standards-Version to reflect concordance with
+ Debian Policy 3.8.2 (no changes needed).
+ - mummer-docs depends on ${misc:Depends}.
+ * debian/patches:
+ - replaces some Makefile patches by environment variables in debian/rules.
+ - replaced 02at_scripts.diff by separate files in sh-replacement-scripts.
-- Charles Plessy <plessy at debian.org> Mon, 19 Jan 2009 09:02:26 +0900
Modified: trunk/packages/mummer/trunk/debian/control
===================================================================
--- trunk/packages/mummer/trunk/debian/control 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/control 2009-06-29 10:43:15 UTC (rev 3572)
@@ -4,8 +4,8 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Andreas Tille <tille at debian.org>, Charles Plessy <plessy 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
+Build-Depends: cdbs, patchutils, debhelper (>= 7), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended
+Standards-Version: 3.8.2
Homepage: http://mummer.sourceforge.net/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mummer/trunk/
@@ -29,6 +29,7 @@
Package: mummer-doc
Architecture: all
Section: doc
+Depends: ${misc:Depends}
Description: Documentation for MUMmer
This package contains the documentation for MUMmer, a system for rapidly
aligning entire genomes.
Modified: trunk/packages/mummer/trunk/debian/copyright
===================================================================
--- trunk/packages/mummer/trunk/debian/copyright 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/copyright 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,7 +1,7 @@
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
+It was downloaded from http://downloads.sourceforge.net/mummer/MUMmer3.21.tar.gz
Copyright: This software is copyright (c) 2000-2007
Copyright Holder: Stefan Kurtz <kurtz at zbh.uni-hamburg.de>,
Modified: trunk/packages/mummer/trunk/debian/mummer.desktop
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.desktop 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/mummer.desktop 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,6 +1,5 @@
[Desktop Entry]
Version=1.0
-Encoding=UTF-8
Terminal=false
Exec=mummer
Name=mummer
Modified: trunk/packages/mummer/trunk/debian/mummer.install
===================================================================
--- trunk/packages/mummer/trunk/debian/mummer.install 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/mummer.install 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,3 +1,3 @@
-bin/* usr/bin
-aux_bin usr/lib/mummer
-scripts/Foundation.pm usr/share/perl5
+debian/tmp/usr/bin/* usr/bin
+debian/tmp/lib/mummer/* usr/lib/mummer
+scripts/Foundation.pm usr/share/perl5
Deleted: trunk/packages/mummer/trunk/debian/patches/01sm_docs.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_docs.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_docs.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,11 +0,0 @@
-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
-
Deleted: trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,98 +0,0 @@
-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
Modified: trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -50,54 +50,3 @@
+ 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)
Deleted: trunk/packages/mummer/trunk/debian/patches/02at_Makefile.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_Makefile.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/02at_Makefile.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,38 +0,0 @@
---- 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
-
-
Modified: trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/02at_docs_web.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,29 +1,48 @@
---- 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 @@
+Description: Some PDFs were removed and have to be downloaded from
+ the upstream website instead.
+Origin: vendor
+Forwarded: not-needed
+--- ./docs/web/index.html.orig 2009-06-29 19:33:23.000000000 +0900
++++ ./docs/web/index.html 2009-06-29 19:34:37.000000000 +0900
+@@ -25,11 +25,11 @@
+ detect similarity, then the PROmer program can generate alignments
+ based upon the six-frame translations of both input sequences. The
+ original MUMmer system, version 1.0, is described in our <a
+- href=MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
++ href=http://mummer.sourceforge.net/MUMmer.pdf>1999 <em>Nucleic Acids Research</em> paper</a>.
+ Version 2.1 appeared a few years later and is described in our <a
+- href=MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
++ href=http://mummer.sourceforge.net/MUMmer2.pdf>2002 <em>Nucleic Acids Research</em> paper</a>,
+ while MUMmer 3.0 was recently described in our <a
+- href=MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
++ href=http://mummer.sourceforge.net/MUMmer3.pdf>2004 <em>Genome Biology</em> paper</a>. For more
+ information regarding the MUMmer package, please refer to the:</p>
+
+ <big><b><a
+@@ -172,7 +172,7 @@
<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>MUMmer 1 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
++ inversions, reported in this <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
+@@ -227,14 +227,14 @@
+ <p><a href="manual">MUMmer 3 user manual</a></p>
+ <p><a href="examples">MUMmer 3 examples</a></p>
<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>."
++ 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
++ <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>."
++ <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
+ <p>Space efficent suffix trees are described in "<a
Deleted: trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff 2009-06-28 12:41:39 UTC (rev 3571)
+++ trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff 2009-06-29 10:43:15 UTC (rev 3572)
@@ -1,241 +0,0 @@
-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
Copied: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh (from rev 3571, trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff)
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh 2009-06-29 10:43:15 UTC (rev 3572)
@@ -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
Property changes on: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh
___________________________________________________________________
Added: svn:mergeinfo
+
Copied: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh (from rev 3571, trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff)
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh 2009-06-29 10:43:15 UTC (rev 3572)
@@ -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
Property changes on: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh
___________________________________________________________________
Added: svn:mergeinfo
+
Copied: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh (from rev 3571, trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff)
===================================================================
--- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh (rev 0)
+++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh 2009-06-29 10:43:15 UTC (rev 3572)
@@ -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
Property changes on: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh
___________________________________________________________________
Added: svn:mergeinfo
+
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