# Maintainer: Mike Dacre <mike@dacre.me>
pkgname=sratoolkit
pkgver=2.4.4
pkgrel=1
pkgdesc="A toolkit from NCBI to download SRA data files and reference sequences and to do file format conversions"
arch=('x86_64')
url="http://www.ncbi.nlm.nih.gov/books/NBK47540/"
license=('custom')
groups=('sequence_analysis')
depends=('bzip2' 'libxml2' 'gcc-libs-multilib' 'fuse' 'curl' 'java-runtime')
source=("http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/$pkgver/sratoolkit.$pkgver-ubuntu64.tar.gz"
        "https://raw.githubusercontent.com/ncbi/sra-tools/master/LICENSE"
        'sratoolkit')

sha1sums=('2aaa090653e4a129b06bcc189c188c9ea77d5f9d'
          '189d29edf32eeec2cf10f5d43b3533207f3f3e87'
          '0a94b50e76a966ee80bd93e55527896df62bddf6')

package() {
  install -d ${pkgdir}/usr/bin
  install -d ${pkgdir}/usr/share/doc/${pkgname}
  install -d ${pkgdir}/usr/share/doc/${pkgname}/example/perl

  cp -r $srcdir/sratoolkit.$pkgver-ubuntu64/bin/* ${pkgdir}/usr/bin/
  #install -Dm755 $srcdir/sratoolkit.$pkgver-ubuntu64/bin/* ${pkgdir}/usr/bin
  #install -Dm755 $srcdir/sratoolkit.$pkgver-ubuntu64/bin/ncbi/* ${pkgdir}/usr/bin/ncbi
  install -Dm755 $srcdir/sratoolkit.$pkgver-ubuntu64/example/perl/* ${pkgdir}/usr/share/doc/${pkgname}/example/perl/

  install -Dm644 $srcdir/sratoolkit.$pkgver-ubuntu64/README* ${pkgdir}/usr/share/doc/${pkgname}

  install -Dm755 $srcdir/sratoolkit ${pkgdir}/usr/bin
  install -Dm644 $srcdir/LICENSE ${pkgdir}/usr/share/licenses/${pkgname}
}