Work in progress PKGBUILD for polyphen

polyphen-PKGBUILD

# Maintainer: Clint Valentine <[email protected]>

pkgname=polyphen
pkgver=2.2.2r405c
pkgrel=1
dbver=2.2.2
blastver=2.7.1
pkgdesc="A tool to predict impact of amino acid substitutions on the structure and function of human proteins"
arch=('any')
url="http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads"
license=('Restricted')
depends=('perl>=5.8.0' 'jre7-openjdk')
provides=('polyphen')
conflicts=('polyphen')
source=(
    "http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/${pkgname}-${pkgver}.tar.gz"
    "ftp://genetics.bwh.harvard.edu/pph2/bundled/${pkgname}-${dbver}-databases-2011_12.tar.bz2"
    "ftp://genetics.bwh.harvard.edu/pph2/bundled/${pkgname}-${dbver}-alignments-mlc-2011_12.tar.bz2"
    "ftp://genetics.bwh.harvard.edu/pph2/bundled/${pkgname}-${dbver}-alignments-multiz-2009_10.tar.bz2"
    "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref100/uniref100.fasta.gz"
    "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/ncbi-blast-${blastver}+-x64-linux.tar.gz"
    "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat"
    "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa"
    "http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz"
    "http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip"
    # There are more databases....
)
md5sums=(
    '82232f41860d1549a0a4c4b25c55fc73'
    'a63eb595c0e308b64b44e5bd9d624950'
    '6cd5921f8f28a92d1c735c1bb03b7e37'
    '5e9900ec919f3bdb9ca40be1b91b1852'
    '396f4e9ef7567ea73e804e9015f27062'
)

prepare() {
    make download
    make clean
}

build() {
  cd "${srcdir}/${pkgname}-${pkgver//r405c/}"
  make

  # ./configure
}

package() {
  cd "${srcdir}/${pkgname}-${pkgver//r405c/}"
  #mkdir -p $pkgdir/usr/bin/
}