version bump

2 files changed, 14 insertions, 17 deletions

diff --git a/.SRCINFO b/.SRCINFO
index b2ca03b295fb..4acaac656169 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,14 +1,16 @@
+# Generated by mksrcinfo v8
+# Fri Jan  5 00:08:52 UTC 2018
 pkgbase = bowtie
 	pkgdesc = Bowtie is an alignment tool for short nucleotide sequences against long templates
-	pkgver = 1.1.2
+	pkgver = 1.2.2
 	pkgrel = 1
 	url = http://bowtie-bio.sf.net
 	arch = x86_64
 	arch = i686
 	license = PerlArtistic
-	source = http://downloads.sourceforge.net/bowtie-bio/bowtie-1.1.2-src.zip
+	source = https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz
 	source = makefile_uname.patch
-	sha256sums = b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae
+	sha256sums = e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1
 	sha256sums = 6b77e333a3ef10e3f787fd2983afd69cdb48e82347fc3316510c2ba5639742a3
 
 pkgname = bowtie
diff --git a/PKGBUILD b/PKGBUILD
index 2d14274101bf..55be30cf451a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,35 +1,30 @@
 # Maintainer: Athemis <alexander.minges[at]googlemail[dot]com>
 # Contributor: sauliusl
 pkgname=bowtie
-pkgver=1.1.2
+pkgver=1.2.2
 pkgrel=1
 pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates"
 url="http://bowtie-bio.sf.net"
 arch=('x86_64' 'i686')
 license=('PerlArtistic')
 depends=()
-source=("http://downloads.sourceforge.net/bowtie-bio/${pkgname}-${pkgver}-src.zip"
+source=("https://github.com/BenLangmead/bowtie/archive/v${pkgver}_p1.tar.gz"
         "makefile_uname.patch")
-sha256sums=('b1e9ccc825207efd1893d9e33244c681bcb89b9b2b811eb95a9f5a92eab637ae'
+sha256sums=('e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1'
             '6b77e333a3ef10e3f787fd2983afd69cdb48e82347fc3316510c2ba5639742a3')
 
 build() {
-  cd "${srcdir}/${pkgname}-${pkgver}"
+  cd "${srcdir}/${pkgname}-${pkgver}_p1"
   patch -Np0 -i ../makefile_uname.patch
-  make
+  make NO_TBB=1 EXTRA_CXXFLAGS="-std=c++03"
 }
 
 package() {
-  cd "${srcdir}/${pkgname}-${pkgver}"
-  install -d ${pkgdir}/usr/bin
+  cd "${srcdir}/${pkgname}-${pkgver}_p1"
+  make prefix=/usr DESTDIR="${pkgdir}" install
   install -d ${pkgdir}/usr/share/doc/${pkgname}
-  install -Dm755 bowtie ${pkgdir}/usr/bin
-  install -Dm755 bowtie-build* ${pkgdir}/usr/bin
-  install -Dm755 bowtie-inspect* ${pkgdir}/usr/bin
-  install -Dm755 bowtie-align* ${pkgdir}/usr/bin
-  install -Dm755 scripts/* ${pkgdir}/usr/bin
-  install -Dm644 doc/* ${pkgdir}/usr/share/doc/${pkgname}
-  install -Dm644 TUTORIAL "${pkgdir}/usr/share/doc/${pkgname}/TUTORIAL"
+  find doc -type f -exec install -Dm644 "{}" "${pkgdir}/usr/share/doc/${pkgname}" \;
+  install -Dm644 TUTORIAL "${pkgdir}/usr/share/doc/$pkgname/TUTORIAL"
   install -Dm644 MANUAL "$pkgdir/usr/share/doc/$pkgname/MANUAL"
   install -Dm644 MANUAL.markdown "$pkgdir/usr/share/doc/$pkgname/MANUAL.markdown"
   install -Dm644 LICENSE "$pkgdir/usr/share/licenses/$pkgname/LICENSE"