tophat-2.1.1-1

3 files changed, 12 insertions, 54 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 0143b0049164..21a3b1b71a3e 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,9 @@
+# Generated by mksrcinfo v8
+# Wed Mar 23 13:58:02 UTC 2016
 pkgbase = tophat
 	pkgdesc = fast splice junction mapper for RNA-Seq reads
-	pkgver = 2.1.0
-	pkgrel = 3
+	pkgver = 2.1.1
+	pkgrel = 1
 	url = http://ccb.jhu.edu/software/tophat/index.shtml
 	arch = x86_64
 	arch = i686
@@ -10,12 +12,8 @@ pkgbase = tophat
 	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 = 34afa379b030c6672a31bbe3689745bc
-	md5sums = 7b0080b01feeb223e054dabef53d6fc5
-	md5sums = 93d47e54408b7b5eb4132d65f5dd5085
+	source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
+	md5sums = 4b2391de46457ba6b2b7268a9da593e4
 
 pkgname = tophat
 
diff --git a/PKGBUILD b/PKGBUILD
index 9494bceb596f..b7d6a6d65104 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,29 +1,20 @@
 # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=tophat
-pkgver=2.1.0
-pkgrel=3
+pkgver=2.1.1
+pkgrel=1
 pkgdesc="fast splice junction mapper for RNA-Seq reads"
 arch=('x86_64' 'i686')
 url="http://ccb.jhu.edu/software/tophat/index.shtml"
 license=('custom')
 depends=('boost-libs' 'bowtie2' 'python2')
 makedepends=('boost')
-source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz"
-        'https://github.com/seqan/seqan/archive/seqan-v1.4.2.tar.gz'
-        'fix_build_w_seqan1.4.patch')
-md5sums=('34afa379b030c6672a31bbe3689745bc'
-         '7b0080b01feeb223e054dabef53d6fc5'
-         '93d47e54408b7b5eb4132d65f5dd5085')
+source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz")
+md5sums=('4b2391de46457ba6b2b7268a9da593e4')
 
 prepare() {
   cd $srcdir/$pkgname-$pkgver
 
-  sed -e 's|-gdwarf-2||' \
-      -e '/define.*esyscmd/d' \
-      -e 's/svnversion/Unversioned directory/' \
-      -i configure.ac
-
   sed -e 's|make $(SAMPROG)|make -e $(SAMPROG)|' \
       -i src/Makefile.am
 
@@ -31,16 +22,8 @@ prepare() {
       -i src/bed_to_juncs \
          src/contig_to_chr_coords \
          src/sra_to_solid \
-         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
+         src/tophat-fusion-post \
+         src/tophat.py
 }
 
 build() {
diff --git a/fix_build_w_seqan1.4.patch b/fix_build_w_seqan1.4.patch
deleted file mode 100644
index 7ab7c5af4a78..000000000000
--- a/fix_build_w_seqan1.4.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-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");
-