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-rw-r--r--PKGBUILD12
1 files changed, 8 insertions, 4 deletions
diff --git a/PKGBUILD b/PKGBUILD
index 9f818d45998..0586f0789c6 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,21 +1,25 @@
# Contributor: Sauliusl <luksaulius at gmail>
pkgname=phantompeakqualtools
pkgver=1.1
-pkgrel=1
+pkgrel=2
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')
+depends=('r' 'r-cran-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
+ tar -xzf spp_1.10.1.tar.gz
+ # Below is requried for this to work with gcc6
+ sed -i "s/PKG_CXXFLAGS=/PKG_CXXFLAGS=-std=gnu++98 /g" spp/src/Makevars.in
+
+ R CMD INSTALL -l $pkgdir/usr/lib/R/library spp
install -d $pkgdir/usr/share/${pkgname}/
install -Dm0644 run_spp.R $pkgdir/usr/share/${pkgname}/