[lilac] updated to 2.2.2.20190706.162801-2

3 files changed, 55 insertions, 65 deletions

diff --git a/.AURINFO b/.AURINFO
deleted file mode 100644
index a4cf8ab5ecf1..000000000000
--- a/.AURINFO
+++ /dev/null
@@ -1,16 +0,0 @@
-pkgbase = cufflinks
-	pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples..
-	pkgver = 2.2.1
-	pkgrel = 1
-	url = http://cufflinks.cbcb.umd.edu
-	arch = x86_64
-	license = Artistic
-	depends = boost
-	depends = eigen3
-	depends = python2
-	depends = samtools
-	depends = perl
-	source = http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz
-
-pkgname = cufflinks
-
diff --git a/.SRCINFO b/.SRCINFO
index c61ed13a914c..174d628e6eec 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,24 @@
 pkgbase = cufflinks
-	pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples..
-	pkgver = 2.2.1
-	pkgrel = 5
-	url = http://cole-trapnell-lab.github.io/projects/cufflinks/
+	pkgdesc = Transcriptome assembly and differential expression analysis for RNA-Seq.
+	pkgver = 2.2.2.20190706.162801
+	pkgrel = 2
+	url = http://cole-trapnell-lab.github.io/cufflinks/
 	arch = x86_64
-	license = Artistic
-	depends = boost
-	depends = eigen3
-	depends = python2
-	depends = samtools
-	depends = perl
-	source = https://github.com/cole-trapnell-lab/cufflinks/archive/v2.2.1.tar.gz
-	md5sums = 80328ff4169f2778c0728a4795da85e2
+	license = BSL
+	makedepends = autoconf
+	makedepends = make
+	makedepends = ncurses
+	makedepends = boost
+	makedepends = eigen
+	makedepends = git
+	makedepends = samtools
+	makedepends = htslib
+	depends = python
+	depends = htslib
+	depends = boost-libs
+	source = git+https://github.com/cole-trapnell-lab/cufflinks.git
+	source = cufflinks.patch::https://github.com/cole-trapnell-lab/cufflinks/pull/108.patch
+	sha1sums = SKIP
+	sha1sums = 081021851cfcc0372bcf1f2e56aa11d0a3b5862c
 
 pkgname = cufflinks
-
diff --git a/PKGBUILD b/PKGBUILD
index 9a364566836a..dab02ecb5cc3 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,49 +1,48 @@
-# Maintainer: Grey Christoforo <first name @ last name .net>
+# Maintainer: Guoyi Zhang <myname at malacology dot net>
+# Contributor: Charles E. Vejnar <ce@vejnar.org>
 
 pkgname=cufflinks
-pkgver=2.2.1
-pkgrel=5
-pkgdesc="Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.."
+_realname=cufflinks
+pkgver=2.2.2.20190706.162801
+pkgrel=2
+pkgdesc="Transcriptome assembly and differential expression analysis for RNA-Seq."
+url="http://cole-trapnell-lab.github.io/cufflinks/"
 arch=("x86_64")
-url="http://cole-trapnell-lab.github.io/projects/cufflinks/"
-license=('Artistic')
-depends=('boost' 'eigen3' 'python2' 'samtools' 'perl')
-source=(https://github.com/cole-trapnell-lab/${pkgname}/archive/v${pkgver}.tar.gz)
-md5sums=('80328ff4169f2778c0728a4795da85e2')
+license=("BSL")
+depends=('python' 'htslib' 'boost-libs')
+makedepends=('autoconf' 'make' 'ncurses' 'boost' 'eigen' 'git' 'samtools' 'htslib')
+source=("git+https://github.com/cole-trapnell-lab/cufflinks.git"
+	"$pkgname.patch::https://github.com/cole-trapnell-lab/cufflinks/pull/108.patch")
+sha1sums=('SKIP'
+          '081021851cfcc0372bcf1f2e56aa11d0a3b5862c')
 
+pkgver () {
+    cd "$srcdir/$pkgname"
+    printf "$(cat configure.ac | grep 'AC_INIT' | sed "s@\[@@g;s@\]@@g;s@,@@g" | awk '{print $2}').%s" "$(TZ=UTC git log -1 --pretty='%cd' --date=format-local:%Y%m%d.%H%M%S)"
+}
 
 prepare() {
-  cd $srcdir/$pkgname-$pkgver
- 
-  sed -i 's,hash\[pos\]\.hash,(hash[pos].hash),g' src/GHash.hh
-  
-  curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/305ee7ba4fa8e8df095d293b9e0827c6a85679a8.patch | patch -p1
-  curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/6c62baa6a9f3a00b71c8fc8f7f4059a7fe49824.patch | patch -p1 
-  
-  curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/87/commits/b7313fffc9d1e3dc92ce8a90b0dd5b2e16cfd68f.patch | patch -p1  
-  
-  #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/d1fdcfd1441d1a8c3b5ecaa1b60a4ae876350061.patch | patch -p1
-  #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/80219fc315208adb4941a20701d68c25f56db756.patch | patch -p1
-
-  curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/107/commits/7aa2922ab1f4ff600bd6854cdebb4be6d3b06fa5.patch | patch -p1
-  
-  ./autogen.sh
-  # cufflinks uses python2 but archlinux uses python3 as default python
-  perl -i -pne '$_ =~ s/python/python2/ if $_ =~ /^#!\/usr/' src/cuffmerge
-
-  export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
-  export LDFLAGS="-L/usr/lib -lboost_system"
-  ./configure --prefix=/usr
+  cd $srcdir/$pkgname
+# for 2.2.1
+#  sed -i "16d" configure.ac
+#  sed -i "s@bam/sam.h@htslib/sam.h@g" src/hits.h
+#  sed -i "s@boost/tr1/unordered_map.hpp@boost/unordered_map.hpp@g" src/biascorrection.h
+  sed -i "17d" configure.ac
+  sed -i "s@sprintf((char \*)vdptr(vs),cmdline);@sprintf((char \*)vdptr(vs),\"%s\",cmdline);@g" src/locfit/makecmd.c
+  sed -i "s@int curwin;@extern int curwin;@g" src/locfit/startlf.c
+  patch -p1 < $srcdir/$pkgname.patch 
 }
 
 build() {
-  cd $srcdir/$pkgname-$pkgver
-  export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
-  export LDFLAGS="-L/usr/lib -lboost_system"
-  make
+  cd $srcdir/$pkgname
+  autoreconf --install
+  ./configure --prefix=/usr --with-boost --with-eigen --with-bam \
+  LIBS="-lboost_system -lboost_thread -lboost_serialization"
+  make CXXFLAGS="-I/usr/include/eigen3 -I/usr/include/htslib/ -std=c++11 -lhts -lpthread"
 }
 
 package() {
-	  cd "$srcdir/$pkgname-$pkgver"
-	  make DESTDIR="$pkgdir/" install
+    cd "$srcdir/$pkgname"
+    make install DESTDIR="$pkgdir"
+    install -Dm 644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
 }