qualimap to sha256sums

2 files changed, 31 insertions, 39 deletions

diff --git a/.SRCINFO b/.SRCINFO
index da34f8ac8f86..3b5dc5091717 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,16 @@
 pkgbase = qualimap
-	pkgdesc = Evaluating next generation sequencing data
+	pkgdesc = Utility to evaluate the quality of next-generation sequencing data
 	pkgver = 2.2.1
-	pkgrel = 1
-	url = http://qualimap.bioinfo.cipf.es/
+	pkgrel = 2
+	url = https://qualimap.bioinfo.cipf.es
 	install = qualimap.install
-	arch = i686
-	arch = x86_64
+	arch = any
 	license = GPL2
-	depends = r>=3.1 java-runtime>=6 java-runtime-openjdk>=6
-	provides = qualimap
-	conflicts = qualimap
-	source = https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip
-	md5sums = a13afe4325ec2f9a065f48a7f0880280
+	depends = r
+	depends = java-runtime>=6
+	depends = java-runtime-openjdk>=6
+	source = http://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1.zip
+	sha256sums = 08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045
 
 pkgname = qualimap
 
diff --git a/PKGBUILD b/PKGBUILD
index 3224f126352a..558fff068328 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,40 +1,33 @@
 # Maintainer: Clint Valentine <valentine.clint@gmail.com>
 pkgname=qualimap
 pkgver=2.2.1
-pkgrel=1
-pkgdesc="Evaluating next generation sequencing data"
-arch=('i686' 'x86_64')
-url="http://qualimap.bioinfo.cipf.es/"
+pkgrel=2
+pkgdesc="Utility to evaluate the quality of next-generation sequencing data"
+arch=('any')
+url=https://qualimap.bioinfo.cipf.es
 license=('GPL2')
-depends=('r>=3.1 java-runtime>=6 java-runtime-openjdk>=6')
-provides=('qualimap')
-conflicts=('qualimap')
+depends=('r' 'java-runtime>=6' 'java-runtime-openjdk>=6')
 install="${pkgname}".install
-source=("https://bitbucket.org/kokonech/${pkgname}/downloads/${pkgname}_v${pkgver}.zip")
-md5sums=('a13afe4325ec2f9a065f48a7f0880280')
+source=(http://bitbucket.org/kokonech/"${pkgname}"/downloads/"${pkgname}"_"v${pkgver}".zip)
+sha256sums=('08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045')
 
-package() {
-  mkdir -p "${pkgdir}/usr/bin/"
-  mkdir -p "${pkgdir}/usr/share/${pkgname}_v${pkgver}"
-  mkdir -p "${pkgdir}/usr/share/licenses/${pkgname}_v${pkgver}/"
-
-  cd "$srcdir/${pkgname}_v${pkgver}"
-
-  ## Set qualimap home environmental default
-  sed -i s#'QUALIMAP_HOME=.*'#'QUALIMAP_HOME=/usr/share/'"${pkgname}"'_v'"${pkgver}"# qualimap
-  install -D -m 775 qualimap "${pkgdir}/usr/bin/qualimap"
+prepare() {
+  cd "${srcdir}"/"${pkgname}"_v"${pkgver}"
+  sed -i s#'QUALIMAP_HOME=.*'#QUALIMAP_HOME=/usr/share/"${pkgname}"_v"${pkgver}"# "${pkgname}"
+}
 
-  # Install license and history
-  install -D -m644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}_v${pkgver}/LICENSE"
-  install -D -m644 HISTORY "${pkgdir}/usr/share/licenses/${pkgname}_v${pkgver}/HISTORY"
+package() {
+  cd "${srcdir}"/"${pkgname}"_v"${pkgver}"
 
-  # Copy .jar library dependencies and .R scripts
-  cp -rf 'lib/'     "${pkgdir}/usr/share/${pkgname}_v${pkgver}/lib"
-  cp -rf 'scripts/' "${pkgdir}/usr/share/${pkgname}_v${pkgver}/scripts"
+  install -Dm644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"/LICENSE
+  install -Dm644 HISTORY "${pkgdir}"/usr/share/licenses/"${pkgname}"/HISTORY
 
-  # Copy species data files
-  cp -rf 'species/' "${pkgdir}/usr/share/${pkgname}_v${pkgver}/species"
+  # Install .jar dependencies, .R scripts, and packaged data.
+  mkdir -p "${pkgdir}"/usr/share/"${pkgname}"
+  cp -rf lib/     "${pkgdir}"/usr/share/"${pkgname}"/lib
+  cp -rf scripts/ "${pkgdir}"/usr/share/"${pkgname}"/scripts
+  cp -rf species/ "${pkgdir}"/usr/share/"${pkgname}"/species
 
-  # Copy the main .jar class
-  cp -f qualimap.jar "${pkgdir}/usr/share/${pkgname}_v${pkgver}/qualimap.jar"
+  install -Dm775 "${pkgname}" "${pkgdir}"/usr/bin/"${pkgname}"
+  install -Dm644 "${pkgname}".jar "${pkgdir}"/usr/share/"${pkgname}"/"${pkgname}".jar
 }