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author | Christian Krause | 2016-03-23 14:58:16 +0100 |
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committer | Christian Krause | 2016-03-23 14:58:16 +0100 |
commit | 1058cf08d5e6449bf7bf9d4b44b3e0883169d069 (patch) | |
tree | 5fde5d7d870a56f914aeec6caa71da2061eeefa5 | |
parent | 80af243f377cb9d7af89d5bdd2b50765a6cb0474 (diff) | |
download | aur-1058cf08d5e6449bf7bf9d4b44b3e0883169d069.tar.gz |
tophat-2.1.1-1
-rw-r--r-- | .SRCINFO | 14 | ||||
-rw-r--r-- | PKGBUILD | 29 | ||||
-rw-r--r-- | fix_build_w_seqan1.4.patch | 23 |
3 files changed, 12 insertions, 54 deletions
@@ -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 @@ -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"); - |