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# Maintainer: Malacology <guoyizhang at malacology dot com>
# Contributor: Malacology <guoyizhang at malacology dot com>
pkgname=easycodeml
pkgver=1.21
pkgrel=1
pkgdesc="A visual tool for analysis of selection using CodeML"
arch=('x86_64')
url="https://github.com/BioEasy/EasyCodeML"
license=('unknow')
source=("https://github.com/starsareintherose/easycodeml/releases/download/${pkgver}/EasyCodeML.zip" "easycodeml.desktop" "EasyCodeML.png")
sha256sums=('45ef18a896818643908dc3ad637da7773f6d984e75f8a6faa61992a7d8e48776'
'e20af3e0e14be4f95d634bf5c34cb35dc37edfada7d97f9c0e9dd10afa7cbf6f'
'5393db9477bd071511788ea6255c49005274b4aebe792a7631eaa296ada14987')
depends=(
'jre-openjdk-headless'
'jre-openjdk'
'jdk-openjdk'
'openjdk-doc'
'openjdk-src'
)
package() {
mkdir "${pkgdir}/usr"
mkdir "${pkgdir}/usr/share"
mkdir "${pkgdir}/usr/share/applications"
mkdir "${pkgdir}/usr/share/EasyCodeML"
mkdir "${pkgdir}/usr/share/EasyCodeML/Custom"
mkdir "${pkgdir}/usr/share/EasyCodeML/Custom/dat"
mkdir "${pkgdir}/usr/share/EasyCodeML/CodeMLSrc"
mkdir "${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/Linux"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BM"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BM/BM"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BM/FR"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BM/M0"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BSM"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BSM/ModelA"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/BSM/ModelAnull"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/CM"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/CM/M22"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/CM/CmC"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M0"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M1a"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M2a"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M3"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M7"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M8"
mkdir "${pkgdir}/usr/share/EasyCodeML/Preset/SM/M8a"
install -m 755 ${srcdir}/EasyCodeML/EasyCodeML.jar ${pkgdir}/usr/share/EasyCodeML/EasyCodeML.jar
install -m 755 ${srcdir}/EasyCodeML/Quick_Guide.pdf ${pkgdir}/usr/share/EasyCodeML/Quick_Guide.pdf
install -m 755 ${srcdir}/EasyCodeML/README.md ${pkgdir}/usr/share/EasyCodeML/README.md
install -m 755 "${srcdir}/EasyCodeML/Version History.txt" "${pkgdir}/usr/share/EasyCodeML/Version History.txt"
install -m 755 ${srcdir}/EasyCodeML/Citation.ris ${pkgdir}/usr/share/EasyCodeML/Citation.ris
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/chi2.c ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/chi2.c
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/chi2.c ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/chi2.c
install -m 755 "${srcdir}/EasyCodeML/CodeMLSrc/Compile Commands for Mac or Linux" "${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/Compile Commands for Mac or Linux"
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/paml.h ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/paml.h
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/tools.c ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/tools.c
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/treespace.c ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/treespace.c
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/treesub.c ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/treesub.c
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/Linux/chi2.exe ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/Linux/chi2.exe
install -m 755 ${srcdir}/EasyCodeML/CodeMLSrc/Linux/codeml.exe ${pkgdir}/usr/share/EasyCodeML/CodeMLSrc/Linux/codeml.exe
install -m 755 ${srcdir}/EasyCodeML/Custom/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Custom/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Custom/default.ctl ${pkgdir}/usr/share/EasyCodeML/Custom/default.ctl
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/cpREV10.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/cpREV10.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/cpREV64.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/cpREV64.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/dayhoff.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/dayhoff.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/dayhoff-dcmut.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/dayhoff-dcmut.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/g1974a.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/g1974a.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/g1974c.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/g1974c.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/g1974p.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/g1974p.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/g1974v.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/g1974v.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/grantham.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/grantham.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/jones.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/jones.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/jones-dcmut.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/jones-dcmut.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/lg.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/lg.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/miyata.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/miyata.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/mtArt.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/mtArt.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/mtmam.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/mtmam.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/mtREV24.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/mtREV24.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/MtZoa.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/MtZoa.dat
install -m 755 ${srcdir}/EasyCodeML/Custom/dat/wag.dat ${pkgdir}/usr/share/EasyCodeML/Custom/dat/wag.dat
install -m 755 ${srcdir}/EasyCodeML/Preset/chi2.exe ${pkgdir}/usr/share/EasyCodeML/Preset/chi2.exe
install -m 755 ${srcdir}/EasyCodeML/Preset/codeml.exe ${pkgdir}/usr/share/EasyCodeML/Preset/codeml.exe
# install -m 755 ${srcdir}/EasyCodeML/Preset/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/.DS_Store
# install -m 755 ${srcdir}/EasyCodeML/Preset/BM/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BM/.DS_Store
# install -m 755 ${srcdir}/EasyCodeML/Preset/BM/BM/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BM/BM/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/BM/BM/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/BM/BM/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/BM/FR/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BM/FR/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/BM/FR/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/BM/FR/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/BM/M0/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BM/M0/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/BM/M0/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/BM/M0/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/BSM/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BSM/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/BSM//ModelA/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/BSM/ModelA/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/BSM/ModelAnull/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/BSM/ModelAnull/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/BSM/ModelAnull/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/BSM/ModelAnull/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/CM/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/CM/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/CM/CmC/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/CM/CmC/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/CM/M22/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/CM/M22/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/SM/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/SM/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M0/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M0/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M1a/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M1a/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M2a/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M2a/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M3/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M3/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M7/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M7/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M8/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M8/codeml.ctl
# install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M8/.DS_Store ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M8/.DS_Store
install -m 755 ${srcdir}/EasyCodeML/Preset/SM/M8a/codeml.ctl ${pkgdir}/usr/share/EasyCodeML/Preset/SM/M8a/codeml.ctl
install -m 755 ${srcdir}/EasyCodeML.png ${pkgdir}/usr/share/EasyCodeML/EasyCodeML.png
install -m 755 ${srcdir}/easycodeml.desktop ${pkgdir}/usr/share/applications/easycodeml.desktop
}
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