tophat-2.1.0-2

3 files changed, 45 insertions, 10 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 44ed614e366c..65a142cead42 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,21 @@
 pkgbase = tophat
 	pkgdesc = fast splice junction mapper for RNA-Seq reads
 	pkgver = 2.1.0
-	pkgrel = 1
+	pkgrel = 2
 	url = http://ccb.jhu.edu/software/tophat/index.shtml
 	arch = x86_64
 	arch = i686
-	license = BSL
+	license = custom
 	makedepends = boost
 	depends = boost-libs
 	depends = bowtie2
 	depends = python2
 	source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
+	source = https://github.com/seqan/seqan/archive/seqan-v1.4.2.tar.gz
+	source = fix_build_w_seqan1.4.patch
 	md5sums = 1ace6e96fa692af6ed885bad5fe7c4d7
+	md5sums = 7b0080b01feeb223e054dabef53d6fc5
+	md5sums = 93d47e54408b7b5eb4132d65f5dd5085
 
 pkgname = tophat
 
diff --git a/PKGBUILD b/PKGBUILD
index 2505f698f67e..9b4876d624be 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,15 +2,19 @@
 
 pkgname=tophat
 pkgver=2.1.0
-pkgrel=1
+pkgrel=2
 pkgdesc="fast splice junction mapper for RNA-Seq reads"
 arch=('x86_64' 'i686')
 url="http://ccb.jhu.edu/software/tophat/index.shtml"
-license=('BSL')
+license=('custom')
 depends=('boost-libs' 'bowtie2' 'python2')
 makedepends=('boost')
-source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz")
-md5sums=('1ace6e96fa692af6ed885bad5fe7c4d7')
+source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz"
+        'https://github.com/seqan/seqan/archive/seqan-v1.4.2.tar.gz'
+        'fix_build_w_seqan1.4.patch')
+md5sums=('1ace6e96fa692af6ed885bad5fe7c4d7'
+         '7b0080b01feeb223e054dabef53d6fc5'
+         '93d47e54408b7b5eb4132d65f5dd5085')
 
 prepare() {
   cd $srcdir/$pkgname-$pkgver
@@ -30,16 +34,18 @@ prepare() {
          src/tophat.py \
          src/tophat-fusion-post
 
+  # fixes seqan issues
+  rm -rf src/SeqAn-1.3
+  patch -Np1 -i $srcdir/fix_build_w_seqan1.4.patch
+  sed -e "s|-I./SeqAn-1.3|-I$srcdir/seqan-seqan-v1.4.2/core/include|" \
+      -i configure.ac
+
   autoreconf -fi
 }
 
 build() {
   cd $srcdir/$pkgname-$pkgver
 
-  export CC=clang
-  export CXX=clang++
-  export PYTHON=python2
-
   ./configure --prefix=/usr
 
   # do not link against system-installed libbam.a
@@ -53,4 +59,6 @@ package() {
   cd $srcdir/$pkgname-$pkgver
 
   make DESTDIR=$pkgdir install
+
+  install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
 }
diff --git a/fix_build_w_seqan1.4.patch b/fix_build_w_seqan1.4.patch
new file mode 100644
index 000000000000..7ab7c5af4a78
--- /dev/null
+++ b/fix_build_w_seqan1.4.patch
@@ -0,0 +1,23 @@
+Description: Resolves build failure with seqan 1.4
+Bug-Closed: http://bugs.debian.org/733352
+Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
+--- a/src/segment_juncs.cpp
++++ b/src/segment_juncs.cpp
+@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
+     typedef map<uint32_t, IntronMotifs> MotifMap;
+     
+     MotifMap ims;
+-	
+-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+-    
++
++    typedef seqan::ModifiedString<
++                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
++                    seqan::ModReverse>   ConstDnaStringReverseComplement;
++    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
++    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
++     
+     if (talkative)
+         fprintf(stderr, "Collecting potential splice sites in islands\n");
+