[med-svn] r17566 - in trunk/packages/bowtie/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Jul 30 11:40:18 UTC 2014
Author: tille
Date: 2014-07-30 11:40:18 +0000 (Wed, 30 Jul 2014)
New Revision: 17566
Removed:
trunk/packages/bowtie/trunk/debian/get-orig-source
Modified:
trunk/packages/bowtie/trunk/debian/changelog
trunk/packages/bowtie/trunk/debian/copyright
trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch
trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
trunk/packages/bowtie/trunk/debian/rules
Log:
New upstream version (adapted patches); drop debian/get-orig-source but rather remove the SeqAn-1.1 code copy via Files-Excluded
Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/changelog 2014-07-30 11:40:18 UTC (rev 17566)
@@ -1,3 +1,11 @@
+bowtie (1.0.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version (adapted patches)
+ * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
+ copy via Files-Excluded
+
+ -- Andreas Tille <tille at debian.org> Wed, 30 Jul 2014 13:38:25 +0200
+
bowtie (1.0.0-6) unstable; urgency=low
* debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
Modified: trunk/packages/bowtie/trunk/debian/copyright
===================================================================
--- trunk/packages/bowtie/trunk/debian/copyright 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/copyright 2014-07-30 11:40:18 UTC (rev 17566)
@@ -2,6 +2,7 @@
Upstream-Name: Bowtie
Upstream-Contact: Ben Langmead <blangmea at jhsph.edu>
Source: http://sourceforge.net/projects/bowtie-bio/files/bowtie/
+Files-Excluded: SeqAn*
Files: *
Copyright: © 2009-2010 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg
Deleted: trunk/packages/bowtie/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/bowtie/trunk/debian/get-orig-source 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/get-orig-source 2014-07-30 11:40:18 UTC (rev 17566)
@@ -1,22 +0,0 @@
-#!/bin/sh
-# script to download and repack source package of bowtie which comes in zip format
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download | \
- grep "Newest version on remote site is .* local version is .*" | \
- head -n 1 | \
- sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
-
-mkdir -p ../tarballs
-cd ../tarballs
-
-UPSTREAMDIR=${PKG}-${VERSION}
-unzip ../"${UPSTREAMDIR}-src.zip"
-
-## remove copy of SeqAn library - unfortunately the package does not compile
-## with the Debian packaged version 1.2
-#rm -rf "${UPSTREAMDIR}"/SeqAn-1.1
-
-GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}"
-rm -rf "${UPSTREAMDIR}"
-
Modified: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -6,9 +6,9 @@
Last-Update: 2013-04-24
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- bowtie-1.0.0.orig/Makefile
-+++ bowtie-1.0.0/Makefile
-@@ -121,6 +121,9 @@
+--- a/Makefile
++++ b/Makefile
+@@ -133,6 +133,9 @@ ifeq (64,$(BITS))
BITS_FLAG = -m64
endif
Modified: trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -5,9 +5,9 @@
Last-Update: 2013-04-24
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- bowtie-1.0.0.orig/Makefile
-+++ bowtie-1.0.0/Makefile
-@@ -45,7 +45,9 @@
+--- a/Makefile
++++ b/Makefile
+@@ -45,7 +45,9 @@ endif
LINUX = 0
ifneq (,$(findstring Linux,$(shell uname)))
LINUX = 1
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-fix-setBegin-call.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -6,7 +6,7 @@
--- a/pat.h
+++ b/pat.h
-@@ -82,20 +82,20 @@
+@@ -82,20 +82,20 @@ struct ReadBuf {
~ReadBuf() {
clearAll(); reset();
// Prevent seqan from trying to free buffers
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -3,9 +3,9 @@
Last-Update: 2014-03-08
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- bowtie-1.0.0.orig/diff_sample.h
-+++ bowtie-1.0.0/diff_sample.h
-@@ -475,6 +475,8 @@
+--- a/diff_sample.h
++++ b/diff_sample.h
+@@ -475,6 +475,8 @@ static String<T> getDeltaMap(T v, const
return amap;
}
@@ -14,7 +14,7 @@
/**
* Return population count (count of all bits set to 1) of i.
*/
-@@ -487,6 +489,7 @@
+@@ -487,6 +489,7 @@ static unsigned int popCount(T i) {
}
return cnt;
}
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -6,7 +6,7 @@
--- a/aligner.h
+++ b/aligner.h
-@@ -337,7 +337,7 @@
+@@ -337,7 +337,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -15,7 +15,7 @@
int *btCnt = NULL,
AlignerMetrics *metrics = NULL) :
Aligner(true, rangeMode),
-@@ -544,7 +544,7 @@
+@@ -544,7 +544,7 @@ protected:
bool quiet_; // don't print informational/warning info
const int maxBts_;
@@ -24,7 +24,7 @@
int *btCnt_;
AlignerMetrics *metrics_;
};
-@@ -585,7 +585,7 @@
+@@ -585,7 +585,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -33,7 +33,7 @@
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
-@@ -1358,7 +1358,7 @@
+@@ -1358,7 +1358,7 @@ protected:
bool quiet_;
int maxBts_;
@@ -42,7 +42,7 @@
int *btCnt_;
// Range-finding state for first mate
-@@ -1482,7 +1482,7 @@
+@@ -1482,7 +1482,7 @@ public:
bool verbose,
bool quiet,
int maxBts,
@@ -51,7 +51,7 @@
int *btCnt) :
Aligner(true, rangeMode),
refs_(refs),
-@@ -2035,7 +2035,7 @@
+@@ -2035,7 +2035,7 @@ protected:
TDriver* driver_;
// Pool for distributing chunks of best-first path descriptor memory
@@ -62,7 +62,7 @@
bool quiet_;
--- a/aligner_0mm.h
+++ b/aligner_0mm.h
-@@ -32,7 +32,7 @@
+@@ -32,7 +32,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
@@ -71,7 +71,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -124,7 +124,7 @@
+@@ -124,7 +124,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -80,7 +80,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool maqPenalty_;
-@@ -164,7 +164,7 @@
+@@ -164,7 +164,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
@@ -89,7 +89,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -366,7 +366,7 @@
+@@ -366,7 +366,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -100,7 +100,7 @@
const bool reportSe_;
--- a/aligner_1mm.h
+++ b/aligner_1mm.h
-@@ -32,7 +32,7 @@
+@@ -32,7 +32,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -109,7 +109,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -161,7 +161,7 @@
+@@ -161,7 +161,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -118,7 +118,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
-@@ -201,7 +201,7 @@
+@@ -201,7 +201,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -127,7 +127,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -478,7 +478,7 @@
+@@ -478,7 +478,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -138,7 +138,7 @@
const bool reportSe_;
--- a/aligner_23mm.h
+++ b/aligner_23mm.h
-@@ -33,7 +33,7 @@
+@@ -33,7 +33,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -147,7 +147,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -231,7 +231,7 @@
+@@ -231,7 +231,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -156,7 +156,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
const bool maqPenalty_;
-@@ -273,7 +273,7 @@
+@@ -273,7 +273,7 @@ public:
RangeCache *cacheFw,
RangeCache *cacheBw,
uint32_t cacheLimit,
@@ -165,7 +165,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -675,7 +675,7 @@
+@@ -675,7 +675,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -176,7 +176,7 @@
const bool reportSe_;
--- a/aligner_seed_mm.h
+++ b/aligner_seed_mm.h
-@@ -37,7 +37,7 @@
+@@ -37,7 +37,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
@@ -185,7 +185,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool maqPenalty,
-@@ -554,7 +554,7 @@
+@@ -554,7 +554,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -194,7 +194,7 @@
BitPairReference* refs_;
vector<String<Dna5> >& os_;
bool strandFix_;
-@@ -598,7 +598,7 @@
+@@ -598,7 +598,7 @@ public:
RangeCache* cacheFw,
RangeCache* cacheBw,
uint32_t cacheLimit,
@@ -203,7 +203,7 @@
BitPairReference* refs,
vector<String<Dna5> >& os,
bool reportSe,
-@@ -1375,7 +1375,7 @@
+@@ -1375,7 +1375,7 @@ private:
RangeCache *cacheFw_;
RangeCache *cacheBw_;
const uint32_t cacheLimit_;
@@ -214,7 +214,7 @@
const bool reportSe_;
--- a/ebwt_search.cpp
+++ b/ebwt_search.cpp
-@@ -110,7 +110,7 @@
+@@ -110,7 +110,7 @@ static bool strandFix; // attempt to fi
static bool randomizeQuals; // randomize quality values
static bool stats; // print performance stats
static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread
@@ -223,7 +223,7 @@
static bool chunkVerbose; // have chunk allocator output status messages?
static bool recal;
static int recalMaxCycle;
-@@ -221,7 +221,7 @@
+@@ -221,7 +221,7 @@ static void resetOptions() {
randomizeQuals = false; // randomize quality values
stats = false; // print performance stats
chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread
@@ -232,7 +232,7 @@
chunkVerbose = false; // have chunk allocator output status messages?
recal = false;
recalMaxCycle = 64;
-@@ -1202,7 +1202,7 @@
+@@ -1202,7 +1202,7 @@ static void exactSearchWorkerStateful(vo
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -241,7 +241,7 @@
UnpairedExactAlignerV1Factory alSEfact(
ebwt,
NULL,
-@@ -1371,7 +1371,7 @@
+@@ -1371,7 +1371,7 @@ static void mismatchSearchWorkerFullStat
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -250,7 +250,7 @@
Unpaired1mmAlignerV1Factory alSEfact(
ebwtFw,
-@@ -1668,7 +1668,7 @@
+@@ -1668,7 +1668,7 @@ static void twoOrThreeMismatchSearchWork
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -259,7 +259,7 @@
Unpaired23mmAlignerV1Factory alSEfact(
ebwtFw,
&ebwtBw,
-@@ -2101,7 +2101,7 @@
+@@ -2101,7 +2101,7 @@ static void seededQualSearchWorkerFullSt
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -270,7 +270,7 @@
if(stats) {
--- a/ebwt_search_backtrack.h
+++ b/ebwt_search_backtrack.h
-@@ -2724,7 +2724,7 @@
+@@ -2724,7 +2724,7 @@ public:
bool verbose,
bool quiet,
bool mate1,
@@ -279,7 +279,7 @@
int *btCnt) :
SingleRangeSourceDriver<EbwtRangeSource>(
params, rs, fw, sink, sinkPt, os, verbose,
-@@ -2927,7 +2927,7 @@
+@@ -2927,7 +2927,7 @@ public:
bool verbose,
bool quiet,
bool mate1,
@@ -288,7 +288,7 @@
int *btCnt = NULL) :
params_(params),
rs_(rs),
-@@ -2986,7 +2986,7 @@
+@@ -2986,7 +2986,7 @@ protected:
bool verbose_;
bool quiet_;
bool mate1_;
@@ -315,7 +315,7 @@
verbose(verbose_), patid(0), pool_(NULL), cur_(0),
chunkSz_(chunkSz), totSz_(totSz), lim_(totSz/chunkSz),
bits_(lim_), exhaustCrash_(false),
-@@ -38,7 +38,7 @@
+@@ -38,7 +38,7 @@ public:
}
} catch(std::bad_alloc& e) {
ThreadSafe _ts(&gLock);
@@ -324,7 +324,7 @@
<< totSz << " bytes" << std::endl;
exhausted();
throw 1; // Exit if we haven't already
-@@ -48,7 +48,7 @@
+@@ -48,7 +48,7 @@ public:
/**
* Delete all the pools.
*/
@@ -333,7 +333,7 @@
if(pool_ != NULL) delete[] pool_;
}
-@@ -189,7 +189,7 @@
+@@ -189,7 +189,7 @@ public:
* Initialize a new pool with an initial size of about 'bytes'
* bytes. Exit with an error message if we can't allocate it.
*/
@@ -342,7 +342,7 @@
pool_(pool), name_(name), curPool_(0), cur_(0)
{
assert(pool != NULL);
-@@ -388,7 +388,7 @@
+@@ -388,7 +388,7 @@ protected:
lastCurInPool_.pop_back();
}
@@ -353,7 +353,7 @@
uint32_t curPool_; /// pool we're current allocating from
--- a/range_source.h
+++ b/range_source.h
-@@ -1388,7 +1388,7 @@
+@@ -1388,7 +1388,7 @@ class PathManager {
public:
@@ -362,7 +362,7 @@
branchQ_(verbose, quiet),
cpool(cpool_),
bpool(cpool, "branch"),
-@@ -1637,7 +1637,7 @@
+@@ -1637,7 +1637,7 @@ protected:
public:
@@ -371,7 +371,7 @@
AllocOnlyPool<Branch> bpool; // pool for allocating Branches
AllocOnlyPool<RangeState> rpool; // pool for allocating RangeStates
AllocOnlyPool<Edit> epool; // pool for allocating Edits
-@@ -1811,7 +1811,7 @@
+@@ -1811,7 +1811,7 @@ public:
bool quiet,
bool mate1,
uint32_t minCostAdjustment,
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -7,7 +7,7 @@
--- a/blockwise_sa.h
+++ b/blockwise_sa.h
-@@ -448,8 +448,8 @@
+@@ -448,8 +448,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
@@ -18,7 +18,7 @@
} catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
-@@ -806,7 +806,7 @@
+@@ -806,7 +806,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
// Not the last bucket
assert_lt(_cur, length(_sampleSuffs));
hi = _sampleSuffs[_cur];
@@ -27,7 +27,7 @@
assert_eq(zHi[0], 0);
calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
}
-@@ -815,7 +815,7 @@
+@@ -815,7 +815,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
assert_gt(_cur, 0);
assert_leq(_cur, length(_sampleSuffs));
lo = _sampleSuffs[_cur-1];
@@ -38,7 +38,7 @@
calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
--- a/diff_sample.h
+++ b/diff_sample.h
-@@ -451,7 +451,7 @@
+@@ -451,7 +451,7 @@ static String<T> getDeltaMap(T v, const
// Declare anchor-map-related items
String<T> amap;
size_t amapEnts = 1;
@@ -47,7 +47,7 @@
amap[0] = 0;
// Print out difference cover (and optionally calculate
// anchor map)
-@@ -531,7 +531,7 @@
+@@ -531,7 +531,7 @@ public:
assert_gt(_d, 0);
assert_eq(1, popCount(_v)); // must be power of 2
// Build map from d's to idx's
@@ -56,7 +56,7 @@
for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
}
-@@ -652,7 +652,7 @@
+@@ -652,7 +652,7 @@ void DifferenceCoverSample<TStr>::doBuil
VMSG_NL(" Doing sanity check");
uint32_t added = 0;
String<uint32_t> sorted;
@@ -65,7 +65,7 @@
for(size_t di = 0; di < this->d(); di++) {
uint32_t d = _ds[di];
size_t i = 0;
-@@ -713,7 +713,7 @@
+@@ -713,7 +713,7 @@ void DifferenceCoverSample<TStr>::buildS
assert_eq(length(_doffs), d+1);
// Size sPrime appropriately
reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
@@ -74,7 +74,7 @@
// Slot suffixes from text into sPrime according to the mu
// mapping; where the mapping would leave a blank, insert a 0
uint32_t added = 0;
-@@ -818,7 +818,7 @@
+@@ -818,7 +818,7 @@ void DifferenceCoverSample<TStr>::build(
// arrays back into sPrime.
VMSG_NL(" Allocating rank array");
reserve(_isaPrime, length(sPrime)+1, Exact());
Modified: trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -6,7 +6,7 @@
--- a/Makefile
+++ b/Makefile
-@@ -173,7 +173,7 @@
+@@ -195,7 +195,7 @@ DEFS=-fno-strict-aliasing \
$(MM_DEF) \
$(SHMEM_DEF)
Modified: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2014-07-30 11:40:18 UTC (rev 17566)
@@ -13,9 +13,9 @@
-SEQAN_DIR = SeqAn-1.1
+SEQAN_DIR = /usr/include/seqan
SEQAN_INC = -I $(SEQAN_DIR)
- INC = $(SEQAN_INC)
+ INC = $(SEQAN_INC) -I third_party
CPP = g++
-@@ -133,7 +133,6 @@
+@@ -151,7 +151,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
Modified: trunk/packages/bowtie/trunk/debian/rules
===================================================================
--- trunk/packages/bowtie/trunk/debian/rules 2014-07-30 10:17:18 UTC (rev 17565)
+++ trunk/packages/bowtie/trunk/debian/rules 2014-07-30 11:40:18 UTC (rev 17566)
@@ -39,4 +39,4 @@
dh_auto_clean
get-orig-source:
- . debian/get-orig-source
+ uscan --verbose --force-download --repack --compress xz
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