[med-svn] r6463 - in trunk/packages/velvet/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Apr 5 13:54:33 UTC 2011
Author: tille
Date: 2011-04-05 13:54:26 +0000 (Tue, 05 Apr 2011)
New Revision: 6463
Added:
trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch
trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch
Removed:
trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff
Modified:
trunk/packages/velvet/trunk/debian/changelog
trunk/packages/velvet/trunk/debian/compat
trunk/packages/velvet/trunk/debian/control
trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
trunk/packages/velvet/trunk/debian/patches/series
trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
trunk/packages/velvet/trunk/debian/rules
Log:
New upstream version, adapted patches to this new version; debhlper 8; prepare building of meta-velvet (whatever this is - needs to be clarified); TODO: exclude contrib/MetaVelvet-v0.3.1 directory from binary package ... and clarify the sense of meta-velvet (separate binary package????)
Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/changelog 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,3 +1,16 @@
+velvet (1.1.02~nozlibcopy-1) UNRELEASED; urgency=low
+
+ * New upstream version
+ upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable
+ of Makefile which makes patch more robust against upstream
+ changes
+ * Debhelper 8 (control+compat)
+ * debian/rules: Leave out Z_LIB_FILES in parameter list
+ * debian/patches/meta-velvet.patch: Enable building meta-velvet
+ in contrib
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 Apr 2011 14:18:24 +0200
+
velvet (1.0.18~nozlibcopy-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/velvet/trunk/debian/compat
===================================================================
--- trunk/packages/velvet/trunk/debian/compat 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/compat 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/control 2011-04-05 13:54:26 UTC (rev 6463)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: cdbs, debhelper (>= 7.1), zlib1g-dev, help2man, quilt
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev, help2man, quilt
Standards-Version: 3.9.1
Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/velvet/trunk/?rev=0&sc=0
Modified: trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,8 +1,8 @@
Description: s?/usr/local/perl?/usr/perl?
Author: Andreas Tille <tille at debian.org>
Forwarded: No
---- velvet_1.0.15~nozlibcopy.orig/contrib/select_paired/select_paired.pl
-+++ velvet_1.0.15~nozlibcopy/contrib/select_paired/select_paired.pl
+--- velvet_1.1.02~nozlibcopy.orig/contrib/select_paired/select_paired.pl
++++ velvet_1.1.02~nozlibcopy/contrib/select_paired/select_paired.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
Modified: trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,9 +1,9 @@
Description: Use the zlib distributed by Debian, not the one in third-party/zlib-1.2.3/.
Author: Charles Plessy <plessy at debian.org>
Forwarded: no
---- velvet_1.0.02~nozlibcopy.orig/src/readSet.c
-+++ velvet_1.0.02~nozlibcopy/src/readSet.c
-@@ -32,7 +32,7 @@
+--- velvet_1.1.02~nozlibcopy.orig/src/readSet.c
++++ velvet_1.1.02~nozlibcopy/src/readSet.c
+@@ -33,7 +33,7 @@
#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
#else
Deleted: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,53 +0,0 @@
-Author: Matthias Klose <doko at ubuntu.com>
-Description: Enable ld --as-needed (basically by using LIBS instead of LDFLAGS.
- Adding libraries in LDFLAGS is almost always a bad idea.
-Closes: #607582
-
-Index: velvet-1.0.15~nozlibcopy/Makefile
-===================================================================
---- velvet-1.0.15~nozlibcopy.orig/Makefile 2010-12-19 21:09:32.228228999 +0000
-+++ velvet-1.0.15~nozlibcopy/Makefile 2010-12-19 21:10:14.818229004 +0000
-@@ -1,7 +1,7 @@
- CC = gcc
- CFLAGS = -Wall
- DEBUG = -g
--LDFLAGS = -lm
-+LIBS = -lm
- OPT = -O3
- MAXKMERLENGTH=31
- CATEGORIES=2
-@@ -44,26 +44,26 @@
- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
-
- velveth : obj
-- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
-+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) $(LIBS)
-
-
- velvetg : obj
-- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS)
-
- debug : override DEF := $(DEF) -D DEBUG
- debug : cleanobj obj/dbg
-- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-
- color : override DEF := $(DEF) -D COLOR
- color : cleanobj obj_de
-- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-- $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS)
-+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS)
-
- colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
- colordebug : cleanobj obj/dbg_de
-- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-- $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-+ $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-
- objdir:
- mkdir -p obj
Added: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch 2011-04-05 13:54:26 UTC (rev 6463)
@@ -0,0 +1,25 @@
+Author: Matthias Klose <doko at ubuntu.com>
+Description: Enable ld --as-needed (basically by using LIBS instead of LDFLAGS.
+ Adding libraries in LDFLAGS is almost always a bad idea.
+Closes: #607582
+
+--- velvet_1.1.02~nozlibcopy.orig/Makefile
++++ velvet_1.1.02~nozlibcopy/Makefile
+@@ -1,14 +1,15 @@
+ CC = gcc
+ CFLAGS = -Wall
+ DEBUG = -g
+-LDFLAGS = -lm
++LIBS = -lm
+ OPT = -O3
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+
+ Z_LIB_DIR=third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
++# In Debian we do not use local zlib copy, however, we need to add $(LIBS) to compile options and thus we tweak this in here:
++Z_LIB_FILES=$(LIBS)
+
+ # Mac OS users: uncomment the following lines
+ # Z_LIB_FILES=
Added: trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch 2011-04-05 13:54:26 UTC (rev 6463)
@@ -0,0 +1,50 @@
+--- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/Makefile
++++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/Makefile
+@@ -1,14 +1,15 @@
+ CC = gcc
+ CFLAGS = -Wall
+ DEBUG = -g
+-LDFLAGS = -lm
++LIBS = -lm
+ OPT = -O3
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+
+ Z_LIB_DIR=../../third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
++# In Debian we do not use local zlib copy, however, we need to add $(LIBS) to compile options and thus we tweak this in here:
++Z_LIB_FILES=$(LIBS)
+
+ # Mac OS users: uncomment the following lines
+ # Z_LIB_FILES=
+@@ -21,7 +22,7 @@
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+
+-default : cleanobj zlib obj meta-velveth meta-velvetg
++default : cleanobj obj meta-velveth meta-velvetg
+
+ clean :
+ -rm obj/*.o obj/dbg/*.o ./meta-velvet*
+@@ -31,7 +32,8 @@
+ -rm obj/*.o obj/dbg/*.o
+
+ zlib :
+- cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++ # cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++ echo "Use Debian packaged version of zlib"
+
+ meta-velveth : obj
+ $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o meta-velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o $(Z_LIB_FILES)
+--- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/src/readSet.c
++++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/src/readSet.c
+@@ -32,7 +32,7 @@
+ #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+ #include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+ #else
+-#include "../third-party/zlib-1.2.3/zlib.h"
++#include <zlib.h>
+ #endif
+
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
Modified: trunk/packages/velvet/trunk/debian/patches/series
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/series 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/series 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,4 +1,5 @@
include_debians_zlib.patch
shuffleSequences_fasta.patch
fix-perl-path.patch
-ld-as-needed.diff
+ld-as-needed.patch
+meta-velvet.patch
Modified: trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch 2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,8 +1,8 @@
Description: Scripts need to specify interpreter in the first line
Author: Andreas Tille <tille at debian.org>
Forwarded: not yet
---- velvet_1.0.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
-+++ velvet_1.0.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
+--- velvet_1.1.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
++++ velvet_1.1.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
@@ -1,3 +1,4 @@
+#!/usr/bin/python
import sys
Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules 2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/rules 2011-04-05 13:54:26 UTC (rev 6463)
@@ -14,10 +14,10 @@
pkg=velvet
-DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LIBS='-lm -lz' OPT=''
+DEB_MAKE_BUILD_TARGET = obj velveth velvetg LIBS='-lm -lz' OPT=''
build/velvet::
- make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LIBS='-lm -lz' OPT=''
+ make color CFLAGS='$(CFLAGS)' LIBS='-lm -lz' OPT=''
mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
help2man --no-info --name="simple hashing program" \
$(CURDIR)/velveth > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1
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