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+# Contributor: Sauliusl <luksaulius at gmail>
+pkgname=phantompeakqualtools
+pkgver=1.1
+pkgrel=1
+pkgdesc="Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays."
+arch=('i686' 'x86_64')
+url="https://code.google.com/p/phantompeakqualtools/"
+license=('MIT')
+depends=('r' 'r-catools' 'r-snow' 'samtools' 'boost' 'boost-libs')
+source=("https://phantompeakqualtools.googlecode.com/files/ccQualityControl.v.${pkgver}.tar.gz")
+md5sums=('66cfe40711edb914cd0fd69778a54e37')
+
+package() {
+
+ cd $srcdir/phantompeakqualtools
+ install -d $pkgdir/usr/lib/R/library
+
+ R CMD INSTALL -l $pkgdir/usr/lib/R/library spp_1.10.1.tar.gz
+
+ install -d $pkgdir/usr/share/${pkgname}/
+ install -Dm0644 run_spp.R $pkgdir/usr/share/${pkgname}/
+ install -Dm0644 run_spp_nodups.R $pkgdir/usr/share/${pkgname}/
+
+ echo "#!/bin/bash" > run_spp.sh
+ echo 'Rscript /usr/share/phantompeakqualtools/run_spp.R "$@"' >> run_spp.sh
+
+ echo "#!/bin/bash" > run_spp_nodups.sh
+ echo 'Rscript /usr/share/phantompeakqualtools/run_spp_nodups.R "$@"' >> run_spp_nodups.sh
+
+ install -d $pkgdir/usr/bin/
+ install -Dm0755 run_spp.sh $pkgdir/usr/bin/run_spp
+ install -Dm0755 run_spp_nodups.sh $pkgdir/usr/bin/run_spp_nodups
+
+
+}