First commit with PKGBUILD, .install, .SRCINFO

3 files changed, 74 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..da34f8ac8f86
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,17 @@
+pkgbase = qualimap
+	pkgdesc = Evaluating next generation sequencing data
+	pkgver = 2.2.1
+	pkgrel = 1
+	url = http://qualimap.bioinfo.cipf.es/
+	install = qualimap.install
+	arch = i686
+	arch = x86_64
+	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
+
+pkgname = qualimap
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..3224f126352a
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,40 @@
+# 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/"
+license=('GPL2')
+depends=('r>=3.1 java-runtime>=6 java-runtime-openjdk>=6')
+provides=('qualimap')
+conflicts=('qualimap')
+install="${pkgname}".install
+source=("https://bitbucket.org/kokonech/${pkgname}/downloads/${pkgname}_v${pkgver}.zip")
+md5sums=('a13afe4325ec2f9a065f48a7f0880280')
+
+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 "${pkgdir}/usr/bin/qualimap"
+
+  # Install license and history
+  install -D -m644 LICENSE "${pkgdir}/usr/share/licenses/${pkgname}_v${pkgver}/LICENSE"
+  install -D -m644 HISTORY "${pkgdir}/usr/share/licenses/${pkgname}_v${pkgver}/HISTORY"
+
+  # Copy .jar library dependencies and .R scripts
+  cp -rf 'lib/'     "${pkgdir}/usr/share/${pkgname}_v${pkgver}/lib"
+  cp -rf 'scripts/' "${pkgdir}/usr/share/${pkgname}_v${pkgver}/scripts"
+
+  # Copy species data files
+  cp -rf 'species/' "${pkgdir}/usr/share/${pkgname}_v${pkgver}/species"
+
+  # Copy the main .jar class
+  cp -f qualimap.jar "${pkgdir}/usr/share/${pkgname}_v${pkgver}/qualimap.jar"
+}
diff --git a/qualimap.install b/qualimap.install
new file mode 100755
index 000000000000..f6ff14586d54
--- /dev/null
+++ b/qualimap.install
@@ -0,0 +1,17 @@
+post_install() {
+	script=$(cat <<-EOF
+		# CountsQC
+		if(!require("optparse")) { install.packages("optparse", repos = "http://cran.r-project.org") }
+		if(!require("NOISeq")) { source("http://bioconductor.org/biocLite.R"); biocLite("NOISeq") }
+
+		# Epigenetics
+		if(!require("XML")) { install.packages("XML", repos = "http://cran.r-project.org") }
+		if(!require("Repitools")) { source("http://bioconductor.org/biocLite.R"); biocLite("Repitools") }
+		if(!require("Rsamtools")) { source("http://bioconductor.org/biocLite.R"); biocLite("Rsamtools") }
+		if(!require("rtracklayer")) { source("http://bioconductor.org/biocLite.R"); biocLite("rtracklayer") }
+	EOF
+	)
+	echo "${script}" > /tmp/qualimap-install-dependencies.R
+	export R_USER=root
+	Rscript /tmp/qualimap-install-dependencies.R
+}