Author: tille Date: 2010-03-24 21:34:48 +0000 (Wed, 24 Mar 2010) New Revision: 4680
Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 Removed: 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 Modified: trunk/packages/mummer/trunk/debian/changelog trunk/packages/mummer/trunk/debian/control trunk/packages/mummer/trunk/debian/mummer.install trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch trunk/packages/mummer/trunk/debian/rules Log: Fix path problems in several scripts Modified: trunk/packages/mummer/trunk/debian/changelog =================================================================== --- trunk/packages/mummer/trunk/debian/changelog 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/changelog 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,3 +1,22 @@ +mummer (3.22~dfsg-2) unstable; urgency=low + + [ Andreas Tille ] + * Make sure scripts will use the installation path instead of + the temporary build path + Closes: #575105 + * Make real use of debian/sh-replacement-scripts and drop csh + (build-)dependency + * incremented Standards-Version to reflect concordance with Debian Policy + 3.8.4 (no changes needed). + * install tandem-repeat.awk which was lacking from installation + previousely + + [ Charles Plessy ] + * Updated upstream-metadata.yaml to use simple key=value form + instead of BibTeX entry + + -- Andreas Tille <[email protected]> Wed, 24 Mar 2010 17:10:43 +0000 + mummer (3.22~dfsg-1) unstable; urgency=low * New upstream release: Modified: trunk/packages/mummer/trunk/debian/control =================================================================== --- trunk/packages/mummer/trunk/debian/control 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/control 2010-03-24 21:34:48 UTC (rev 4680) @@ -4,15 +4,15 @@ Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]>, Charles Plessy <[email protected]> -Build-Depends: csh, quilt, debhelper (>= 7.0.50), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended -Standards-Version: 3.8.3 +Build-Depends: quilt, debhelper (>= 7.0.50), texlive-latex-base, texlive-latex-recommended, texlive-fonts-recommended +Standards-Version: 3.8.4 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/ Package: mummer Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk, csh +Depends: ${shlibs:Depends}, ${misc:Depends}, perl, gawk 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 Modified: trunk/packages/mummer/trunk/debian/mummer.install =================================================================== --- trunk/packages/mummer/trunk/debian/mummer.install 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/mummer.install 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,3 +1,5 @@ debian/tmp/usr/bin/* usr/bin debian/tmp/usr/lib/mummer/* usr/lib/mummer scripts/Foundation.pm usr/share/perl5 +scripts/tandem-repeat.awk usr/lib/mummer + Modified: trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch =================================================================== --- trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/patches/10_install_dirs.patch 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,5 +1,5 @@ ---- mummer-3.22~dfsg.orig/scripts/Makefile -+++ mummer-3.22~dfsg/scripts/Makefile +--- MUMmer3.22.orig/scripts/Makefile ++++ MUMmer3.22/scripts/Makefile @@ -4,14 +4,19 @@ ifndef BIN_DIR BIN_DIR := $(CURDIR) @@ -21,55 +21,80 @@ SED := $(filter /%,$(shell /bin/sh -c 'type sed')) CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) -@@ -37,7 +42,7 @@ +@@ -35,59 +40,52 @@ + + #-- not so PHONY rules --# - exact-tandems: exact-tandems.csh - $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ +-exact-tandems: exact-tandems.csh +- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ -+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - exact-tandems.csh > $(BIN_DIR)/exact-tandems +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- exact-tandems.csh > $(BIN_DIR)/exact-tandems ++exact-tandems: ../debian/sh-replacement-scripts/exact-tandems ++ cp -a $^ $(BIN_DIR) chmod 755 $(BIN_DIR)/exact-tandems -@@ -51,21 +56,21 @@ + + mapview: mapview.pl + $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ ++ -e 's?__SCRIPT_DIR?$(FINAL_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?$(SCRIPT_DIR)?g' \ +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ ++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(FINAL_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?$(SCRIPT_DIR)?g' \ +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ ++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \ + -e 's?__BIN_DIR?$(FINAL_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?$(SCRIPT_DIR)?g' \ +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ +- -e 's?__BIN_DIR?$(BIN_DIR)?g' \ ++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ ++ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \ nucmer.pl > $(BIN_DIR)/nucmer chmod 755 $(BIN_DIR)/nucmer -@@ -73,14 +78,14 @@ + promer: promer.pl Foundation.pm $(SED) -e 's?__PERL_PATH?$(PERL)?g' \ - -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ +- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \ - -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ ++ -e 's?__SCRIPT_DIR?$(FINAL_SCRIPT_DIR)?g' \ + -e 's?__AUX_BIN_DIR?$(FINAL_AUX_BIN_DIR)?g' \ + -e 's?__BIN_DIR?$(FINAL_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' \ +-run-mummer1: run-mummer1.csh +- $(SED) -e 's?__CSH_PATH?$(CSH)?g' \ - -e 's?__BIN_DIR?$(BIN_DIR)?g' \ -+ -e 's?__BIN_DIR?$(FINAL_BIN_DIR)?g' \ - run-mummer1.csh > $(BIN_DIR)/run-mummer1 +- run-mummer1.csh > $(BIN_DIR)/run-mummer1 ++run-mummer1: ../debian/sh-replacement-scripts/run-mummer1 ++ cp -a $^ $(BIN_DIR) 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 ++run-mummer3: ../debian/sh-replacement-scripts/run-mummer3 ++ cp -a $^ $(BIN_DIR) + chmod 755 $(BIN_DIR)/run-mummer3 + + nucmer2xfig: nucmer2xfig.pl Modified: trunk/packages/mummer/trunk/debian/rules =================================================================== --- trunk/packages/mummer/trunk/debian/rules 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/rules 2010-03-24 21:34:48 UTC (rev 4680) @@ -41,6 +41,9 @@ TMPDIR = $(CURDIR)/debian/tmp BIN_DIR = $(TMPDIR)/usr/bin AUX_BIN_DIR = $(TMPDIR)/usr/lib/mummer +FINAL_BIN_DIR = /usr/bin +FINAL_AUX_BIN_DIR = /usr/lib/mummer +FINAL_SCRIPT_DIR = /usr/share/perl5/ build: $(QUILT_STAMPFN) build-stamp build-stamp: @@ -55,7 +58,10 @@ dh_installdirs [ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR) [ -d $(AUX_BIN_DIR) ] || mkdir -p $(AUX_BIN_DIR) - $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) CFLAGS="$(CFLAGS)" + $(MAKE) BIN_DIR=$(BIN_DIR) AUX_BIN_DIR=$(AUX_BIN_DIR) \ + FINAL_BIN_DIR=$(FINAL_BIN_DIR) FINAL_AUX_BIN_DIR=$(FINAL_AUX_BIN_DIR) \ + FINAL_SCRIPT_DIR=$(FINAL_SCRIPT_DIR) \ + CFLAGS="$(CFLAGS)" $(MAKE) -C docs $(MAKE) check # /usr/bin/annotate renamed /usr/bin/mummer-annotate for namespace and license (Artistic) reasons. Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems (rev 0) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems 2010-03-24 21:34:48 UTC (rev 4680) @@ -0,0 +1,35 @@ +#!/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="$2" + +bindir=/usr/bin +scriptdir=/usr/lib/mummer + +if [ ! -e "$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 $$.tmp.matches Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/exact-tandems.sh 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,34 +0,0 @@ -#!/bin/sh -e -# -# Find exact tandem repeats in specified file involving an -# exact duplicate of at least the specified length - -usage () { - echo "Usage: `basename $0` <file> <min-match-len>" - return 67 # EX_USAGE -} - -if [ $# -ne 2 ] ; then - echo "You provided $# arguments instead of 2." - usage -fi - -filename="$1" -matchlen="$2" - -bindir=__BIN_DIR -scriptdir=__SCRIPT_DIR - -if [ ! -e "$filename" ] ; then - echo "File $filename does not exist." - usage -fi - -echo "Finding matches" -$bindir/repeat-match -t -n $matchlen "$filename" | tail +3 > $$.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 Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 (rev 0) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1 2010-03-24 21:34:48 UTC (rev 4680) @@ -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="$4" + +bindir=/usr/bin + +if [ ! -e "$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 Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer1.sh 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,45 +0,0 @@ -#!/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 Added: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 (rev 0) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3 2010-03-24 21:34:48 UTC (rev 4680) @@ -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="$3" + +bindir=/usr/bin + +if [ ! -e "$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 Deleted: trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh =================================================================== --- trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh 2010-03-24 13:47:00 UTC (rev 4679) +++ trunk/packages/mummer/trunk/debian/sh-replacement-scripts/run-mummer3.sh 2010-03-24 21:34:48 UTC (rev 4680) @@ -1,47 +0,0 @@ -#!/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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
