diff options
-rw-r--r-- | .SRCINFO | 10 | ||||
-rw-r--r-- | PKGBUILD | 28 |
2 files changed, 20 insertions, 18 deletions
@@ -2,15 +2,15 @@ pkgbase = structure pkgdesc = Program for using multi-locus genotype data to investigate population structure. pkgver = 2.3.4 pkgrel = 4 - url = http://pritch.bsd.uchicago.edu/structure.html + url = http://web.stanford.edu/group/pritchardlab/structure.html arch = i686 arch = x86_64 license = GPL makedepends = java-environment - depends = java-runtime=8 - source = http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz - source = http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_frontend_source.tar.gz - source = http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/html/ran.c.patch + depends = java-runtime + source = http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_kernel_source.tar.gz + source = http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_frontend_source.tar.gz + source = http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/ran.c.patch md5sums = 4e0591678cdbfe79347d272b5dceeda1 md5sums = f4b257767562ba732c7a02414fee1865 md5sums = a7c26d216eacb2a10f9ff0fb7e0c31a6 @@ -1,48 +1,50 @@ -# Maintainer: Stunts <f DOT pinamartins AT gmail DOT com> +# Maintainer: Stunts <stunts AT pinamartins DOT com> # Contributor: bmpvieira <mail AT bmpvieira DOT com> pkgname=structure pkgver=2.3.4 pkgrel=4 pkgdesc="Program for using multi-locus genotype data to investigate population structure." arch=('i686' 'x86_64') -url="http://pritch.bsd.uchicago.edu/structure.html" +url="http://web.stanford.edu/group/pritchardlab/structure.html" license=('GPL') -depends=('java-runtime=8') +depends=('java-runtime') makedepends=('java-environment') -source=(http://pritchardlab.stanford.edu/structure_software/release_versions/v${pkgver}/structure_kernel_source.tar.gz - http://pritchardlab.stanford.edu/structure_software/release_versions/v${pkgver}/structure_frontend_source.tar.gz - http://pritchardlab.stanford.edu/structure_software/release_versions/v${pkgver}/html/ran.c.patch) +source=(http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v${pkgver}/structure_kernel_source.tar.gz + http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v${pkgver}/structure_frontend_source.tar.gz + http://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v${pkgver}/html/ran.c.patch) md5sums=('4e0591678cdbfe79347d272b5dceeda1' 'f4b257767562ba732c7a02414fee1865' 'a7c26d216eacb2a10f9ff0fb7e0c31a6') build() { - #Patch for creating random seed in an RW location: + # Patch for creating random seed in an RW location: patch ${srcdir}/structure_kernel_src/ran.c < ran.c.patch - #build core program + # build core program cd ${srcdir}/structure_kernel_src + # force -fcommon to successfully build with GCC > 9.X + sed -i 's/OPT = -O3/OPT = -O3 -fcommon/' Makefile make - #build frontend + # build frontend cd ${srcdir}/structure_frontend_src javac -cp class/Structure.jar RunStructure.java } package() { - #create necessary dirs + # create necessary dirs mkdir -p "${pkgdir}/usr/bin" mkdir -p ${pkgdir}/opt/structure/bin - #copy frontend files + # copy frontend files cp -r ${srcdir}/structure_frontend_src/{class,images,library} ${pkgdir}/opt/structure/ - #copy core program file + # copy core program file cp ${srcdir}/structure_kernel_src/structure ${pkgdir}/opt/structure/bin cd "$pkgdir/opt/structure" - #create launcher script + # create launcher script echo '#!/bin/sh' > structure echo 'cd /opt/structure/' >> structure echo 'java -cp /opt/structure/class/Structure.jar RunStructure' >> structure |