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# Maintainer: Kiri <kiri@vern.cc>
# Contributor: wangzhichao <wangzhichao1990@126.com>
pkgname=bio-tbtools
_pkgname=tbtools
pkgver=2.121
pkgrel=1
epoch=1
pkgdesc='GUI/CommandLine Tool Box for biologistists to utilize NGS data. \
https://doi.org/10.1016/j.molp.2023.09.010'
arch=('x86_64')
url='https://github.com/CJ-Chen/TBtools-II'
license=('unknown')
depends=('java-runtime>=11'
'bash')
makedepends=('unzip'
'gendesk')
optdepends=('blast+: BLAST support'
'diamond: quick blast(needed in quick MCScanx scan) support'
'mcscanx: collinear scan support'
'hmmer: HMM Search support'
'muscle: align support'
'trimal: large scale align support'
'iqtree: maximum likelihood phylogenomic tree support'
'kaks_calculator: kaks calculate support')
source=("https://github.com/CJ-Chen/TBtools-II/releases/download/${pkgver}/TBtools_JRE1.6.jar")
sha256sums=('e0a208906278d315e2e1e81c83415c57bbdeee6c7215a5bb411e463569fae67d')
prepare() {
# generate /usr/bin file
printf '#!/usr/bin/sh\nexec java -jar /usr/share/bio-tbtools/tbtools*.jar "$@"\n'>${srcdir}/${_pkgname}
# generate desk entry
gendesk -f -n --pkgname "${_pkgname}" --pkgdesc "${pkgdesc}" --exec="${_pkgname}" --name="${_pkgname}" --categories="Science"
}
package() {
install -Dm 755 ${srcdir}/${_pkgname} ${pkgdir}/usr/bin/${_pkgname}
install -Dm 644 ${srcdir}/${_pkgname}.desktop ${pkgdir}/usr/share/applications/${_pkgname}.desktop
install -Dm 755 ${srcdir}/TBtools*.jar ${pkgdir}/usr/share/${pkgname}/${_pkgname}.jar
install -Dm 644 ${srcdir}/Icons/TBtoolsLogo.png ${pkgdir}/usr/share/icons/hicolor/720x720/apps/${_pkgname}.png
install -Dm 644 ${srcdir}/Icons/TBtoolsLogo16x16.png ${pkgdir}/usr/share/icons/hicolor/16x16/apps/${_pkgname}.png
}
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