Version 1.3.1

3 files changed, 22 insertions, 44 deletions

diff --git a/.SRCINFO b/.SRCINFO
index c976912c35d5..37b0e9589f0f 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,15 +1,14 @@
 pkgbase = bowtie
-	pkgdesc = Bowtie is an alignment tool for short nucleotide sequences against long templates
-	pkgver = 1.2.3
+	pkgdesc = Alignment tool for short nucleotide sequences against long templates
+	pkgver = 1.3.1
 	pkgrel = 1
-	url = http://bowtie-bio.sf.net
+	url = https://bowtie-bio.sf.net
 	arch = x86_64
 	arch = i686
-	license = PerlArtistic
-	source = https://github.com/BenLangmead/bowtie/archive/v1.2.3.tar.gz
-	source = makefile_uname.patch
-	sha256sums = 86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823
-	sha256sums = 6b77e333a3ef10e3f787fd2983afd69cdb48e82347fc3316510c2ba5639742a3
+	license = Artistic2.0
+	depends = python
+	depends = perl
+	source = bowtie-1.3.1.tar.gz::https://github.com/BenLangmead/bowtie/archive/v1.3.1.tar.gz
+	sha256sums = 147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573
 
 pkgname = bowtie
-
diff --git a/PKGBUILD b/PKGBUILD
index 25a0c7d8b275..2c48e2593d08 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,39 +1,29 @@
-# Maintainer: Athemis <alexander.minges[at]googlemail[dot]com>
+# Maintainer: a821
+# Contributor: Athemis <alexander.minges[at]googlemail[dot]com>
 # Contributor: sauliusl
+
 pkgname=bowtie
-pkgver=1.2.3
+pkgver=1.3.1
 pkgrel=1
-pkgdesc="Bowtie is an alignment tool for short nucleotide sequences against long templates"
-url="http://bowtie-bio.sf.net"
+pkgdesc="Alignment tool for short nucleotide sequences against long templates"
+url="https://bowtie-bio.sf.net"
 arch=('x86_64' 'i686')
-license=('PerlArtistic')
-depends=()
-source=("https://github.com/BenLangmead/bowtie/archive/v${pkgver}.tar.gz"
-        "makefile_uname.patch")
-sha256sums=('86402114caeacbb3a3030509cb59f0b7e96361c7b3ee2dd50e2cd68200898823'
-            '6b77e333a3ef10e3f787fd2983afd69cdb48e82347fc3316510c2ba5639742a3')
-
-prepare() {
-  cd "${srcdir}/${pkgname}-${pkgver}"
-  patch -Np0 -i ../makefile_uname.patch
-}
+license=('Artistic2.0')
+depends=('python' 'perl')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/BenLangmead/bowtie/archive/v${pkgver}.tar.gz")
+sha256sums=('147d9fe9652f7c5f351bfc0eb012e06981986fb43bd6bdfe88a95c02eabc6573')
 
 build() {
   cd "${srcdir}/${pkgname}-${pkgver}"
-  make NO_TBB=1 EXTRA_CXXFLAGS="-std=c++03"
+  make
 }
 
 package() {
   cd "${srcdir}/${pkgname}-${pkgver}"
   make prefix=/usr DESTDIR="${pkgdir}" install
-  install -d ${pkgdir}/usr/share/doc/${pkgname}
-  install -Dm755 scripts/*.pl "${pkgdir}/usr/bin"
-  install -Dm755 scripts/*.sh "${pkgdir}/usr/bin"
-  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"
+
+  install -Dm755 -t "${pkgdir}/usr/share/${pkgname}/scripts/" scripts/*.{pl,sh}
+  install -Dm644 -t "${pkgdir}/usr/share/doc/$pkgname/" MANUAL{,.markdown} TUTORIAL AUTHORS NEWS
 }
 
 # vim:set ts=2 sw=2 et:
diff --git a/makefile_uname.patch b/makefile_uname.patch
deleted file mode 100644
index b9833cd6d4db..000000000000
--- a/makefile_uname.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- Makefile	2013-04-18 21:33:44.000000000 +0200
-+++ Makefile	2013-06-26 16:25:17.622402991 +0200
-@@ -107,7 +107,7 @@
- endif
- 
- ifeq (1,$(LINUX))
--    ifeq (x86_64, $(shell uname -p))
-+    ifeq (x86_64, $(shell uname -m))
-         BITS=64
-     endif
- endif