[lilac] updated to 2.1.2-3

4 files changed, 60 insertions, 31 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 5d35a00b570c..66dc2e3bec69 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,21 +1,21 @@
-# Generated by mksrcinfo v8
-# Thu Jun  2 09:32:08 UTC 2016
 pkgbase = tophat
 	pkgdesc = fast splice junction mapper for RNA-Seq reads
-	pkgver = 2.1.1
-	pkgrel = 2
+	pkgver = 2.1.2
+	pkgrel = 3
 	url = http://ccb.jhu.edu/software/tophat/index.shtml
 	arch = x86_64
 	arch = i686
 	license = custom
 	makedepends = boost
+	makedepends = clang
 	depends = boost-libs
 	depends = bowtie2
-	depends = python2
-	source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
+	depends = python
+	source = tophat-2.1.2.tar.gz::https://github.com/DaehwanKimLab/tophat/archive/refs/tags/v2.1.2.tar.gz
 	source = make_pair.patch
-	md5sums = 4b2391de46457ba6b2b7268a9da593e4
-	md5sums = 53378885f3620a1d02fb345077609d05
+	source = configure.patch
+	md5sums = db844fd7f53c519e716cd6222e6195b2
+	md5sums = 4f53cd3e611c2a0744babede14c3ae66
+	md5sums = 175420b0b08f2979d9585ec55cbeb0ee
 
 pkgname = tophat
-
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
diff --git a/configure.patch b/configure.patch
new file mode 100644
index 000000000000..716b6c003424
--- /dev/null
+++ b/configure.patch
@@ -0,0 +1,19 @@
+--- configure.ac.bak	2018-05-24 23:24:31.000000000 +0800
++++ configure.ac	2022-07-19 10:24:36.805405047 +0800
+@@ -5,7 +5,7 @@
+ AC_CONFIG_SRCDIR([config.h.in])
+ AC_CONFIG_HEADERS([config.h])
+ # AC_CONFIG_AUX_DIR([build-aux])
+-AM_INIT_AUTOMAKE
++AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+
+ AC_ARG_VAR(PYTHON, [python program])
+
+@@ -108,7 +108,6 @@
+ CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
+ LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
+
+-AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
+
+ # makefiles to configure
+ AC_CONFIG_FILES([Makefile src/Makefile])
diff --git a/make_pair.patch b/make_pair.patch
index 44b71d1059ab..0ec41903308b 100644
--- a/make_pair.patch
+++ b/make_pair.patch
@@ -9,14 +9,14 @@ diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.c
 +			junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats()));
  		}
  	}
- 
+
 diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp
 --- tophat-2.1.1/src/tophat_reports.cpp	2016-02-23 22:20:44.320710000 +0100
 +++ tophat-2.1.1-patched/src/tophat_reports.cpp	2016-06-02 11:26:22.057239478 +0200
 @@ -2705,7 +2705,7 @@
  				junction_stat.gtf_match = true;
  				junction_stat.accepted = true;
- 
+
 -				gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
 +				gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat));
  			}