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authorFrancisco Pina Martins2015-06-09 14:10:46 +0100
committerFrancisco Pina Martins2015-06-09 14:10:46 +0100
commit29634fb762b3244275df405545f4c1e7fe9ab8f2 (patch)
treed393a9369406cc39dfa07e523918291c6397c4e3
downloadaur-29634fb762b3244275df405545f4c1e7fe9ab8f2.tar.gz
Initial import.
-rw-r--r--.SRCINFO18
-rw-r--r--PKGBUILD52
2 files changed, 70 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..55228ff9c9cf
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,18 @@
+pkgbase = structure
+ pkgdesc = Program for using multi-locus genotype data to investigate population structure.
+ pkgver = 2.3.4
+ pkgrel = 3
+ url = http://pritch.bsd.uchicago.edu/structure.html
+ arch = i686
+ arch = x86_64
+ license = GPL
+ depends = java-environment
+ 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
+ md5sums = 4e0591678cdbfe79347d272b5dceeda1
+ md5sums = f4b257767562ba732c7a02414fee1865
+ md5sums = a7c26d216eacb2a10f9ff0fb7e0c31a6
+
+pkgname = structure
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..9e7fba25501f
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,52 @@
+# Maintainer: Stunts <f DOT pinamartins AT gmail DOT com>
+# Contributor: bmpvieira <mail AT bmpvieira DOT com>
+pkgname=structure
+pkgver=2.3.4
+pkgrel=3
+pkgdesc="Program for using multi-locus genotype data to investigate population structure."
+arch=('i686' 'x86_64')
+url="http://pritch.bsd.uchicago.edu/structure.html"
+license=('GPL')
+depends=('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)
+md5sums=('4e0591678cdbfe79347d272b5dceeda1'
+ 'f4b257767562ba732c7a02414fee1865'
+ 'a7c26d216eacb2a10f9ff0fb7e0c31a6')
+
+build() {
+ #Patch for creating random seed in an RW location:
+ patch ${srcdir}/structure_kernel_src/ran.c < ran.c.patch
+ #build core program
+ cd ${srcdir}/structure_kernel_src
+ make
+
+ #build frontend
+ cd ${srcdir}/structure_frontend_src
+ javac -cp class/Structure.jar RunStructure.java
+}
+
+package() {
+ #create necessary dirs
+ mkdir -p "${pkgdir}/usr/bin"
+ mkdir -p ${pkgdir}/opt/structure/bin
+
+ #copy frontend files
+ cp -r ${srcdir}/structure_frontend_src/{class,images,library} ${pkgdir}/opt/structure/
+
+ #copy core program file
+ cp ${srcdir}/structure_kernel_src/structure ${pkgdir}/opt/structure/bin
+
+ cd "$pkgdir/opt/structure"
+
+ #create launcher script
+ echo '#!/bin/sh' > structure
+ echo 'cd /opt/structure/' >> structure
+ echo 'java -cp /opt/structure/class/Structure.jar RunStructure' >> structure
+
+ chmod +x ./structure
+ ln -s "/opt/structure/structure" "$pkgdir/usr/bin/structure"
+}
+# vim:set ts=2 sw=2 et: