PKGBUILD for phantompeakqualtoools git version

phantompeakqualtools-git.PKGBUILD

#  This doesn't work nicely as it uses bioclite to install dependdencies
# which is why I'm not submitting it to AUR
# but it's useful if one compiles it themselves.
pkgname=phantompeakqualtools-git
pkgver=r30.b9267ea

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://github.com/kundajelab/phantompeakqualtools"
license=('MIT')
depends=('r' 'r-cran-catools' 'r-snow' 'samtools' 'boost' 'boost-libs')
source=("$pkgname::git+https://github.com/kundajelab/phantompeakqualtools.git")
sha1sums=('SKIP')
conflicts=("phantompeakqualtools")

pkgver() {
  cd "$srcdir/$pkgname"

  #printf "%s" "$(git describe --long | sed 's/\([^-]*-\)g/r\1/;s/-/./g')"
  printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
}

package() {

 cd $srcdir/$pkgname
 install -d $pkgdir/usr/lib/R/library

 # Below is required for this to work with gcc6
tar xvf spp_1.14.tar.gz
sed -i "s/PKG_CXXFLAGS=/PKG_CXXFLAGS=-std=gnu++98 /g" spp-1.14/src/Makevars.in



 R -e "source('https://bioconductor.org/biocLite.R'); biocLite('Rsamtools', lib='${pkgdir}/usr/lib/R/library')"
 R CMD INSTALL -l $pkgdir/usr/lib/R/library spp-1.14

 install -d $pkgdir/usr/share/phantompeakqualtools/
 install -Dm0644 run_spp.R $pkgdir/usr/share/phantompeakqualtools/

 echo "#!/bin/bash" > run_spp.sh
 echo 'Rscript /usr/share/phantompeakqualtools/run_spp.R "$@"' >> run_spp.sh

 install -d $pkgdir/usr/bin/
 install -Dm0755 run_spp.sh $pkgdir/usr/bin/run_spp

}