[lilac] updated to 2.1.2-3

1 files changed, 30 insertions, 20 deletions

diff --git a/PKGBUILD b/PKGBUILD
index e38a5ba93bc9..018b909a30ef 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,18 +1,21 @@
 # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=tophat
-pkgver=2.1.1
-pkgrel=2
+pkgver=2.1.2
+pkgrel=3
 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-$pkgver.tar.gz"
-        'make_pair.patch')
-md5sums=('4b2391de46457ba6b2b7268a9da593e4'
-         '53378885f3620a1d02fb345077609d05')
+depends=('boost-libs' 'bowtie2' 'python')
+makedepends=('boost' 'clang')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DaehwanKimLab/tophat/archive/refs/tags/v${pkgver}.tar.gz"
+        'make_pair.patch'
+        'configure.patch'
+        )
+md5sums=('db844fd7f53c519e716cd6222e6195b2'
+         '4f53cd3e611c2a0744babede14c3ae66'
+         '175420b0b08f2979d9585ec55cbeb0ee')
 
 prepare() {
   cd $srcdir/$pkgname-$pkgver
@@ -20,22 +23,28 @@ prepare() {
   sed -e 's|make $(SAMPROG)|make -e $(SAMPROG)|' \
       -i src/Makefile.am
 
-  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
-      -i src/bed_to_juncs \
-         src/contig_to_chr_coords \
-         src/sra_to_solid \
-         src/tophat-fusion-post \
-         src/tophat.py
+  # sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
+  #     -i src/bed_to_juncs \
+  #        src/contig_to_chr_coords \
+  #        src/sra_to_solid \
+  #        src/tophat-fusion-post \
+  #        src/tophat.py
+
+  # to python3
+  2to3 -w  -n .
 
   patch -Np1 -i $srcdir/make_pair.patch
+  patch -Np0 -i $srcdir/configure.patch
+  autoreconf -i
+  autoupdate
+  autoconf
 }
 
 build() {
   cd $srcdir/$pkgname-$pkgver
-
-  export PYTHON=python2
-
-  ./configure --prefix=/usr
+  export CC=clang
+  export CXX=clang++
+  ./configure --prefix=/usr --with-python-sys-prefix
 
   # do not link against system-installed libbam.a
   sed -e 's|-L/usr/lib||' \
@@ -50,9 +59,10 @@ package() {
   make DESTDIR=$pkgdir install
 
   # fix python install
-  install -d $pkgdir/usr/lib/python2.7/site-packages
+  _pyver=$(python -V | cut -d ' '  -f2)
+  install -d $pkgdir/usr/lib/python${_pyver:0:4}/site-packages
   mv \
-    -t $pkgdir/usr/lib/python2.7/site-packages \
+    -t $pkgdir/usr/lib/python${_pyver:0:4}/site-packages \
     $pkgdir/usr/bin/{intervaltree,sortedcontainers}
 
   install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE