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-rw-r--r--.SRCINFO19
-rw-r--r--PKGBUILD33
-rw-r--r--snpeff2
-rw-r--r--snpsift2
4 files changed, 56 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 00000000000..56c0a4e76af
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,19 @@
+pkgbase = snpeff
+ pkgdesc = Genetic variant annotation and effect prediction toolbox
+ pkgver = 4_3t
+ pkgrel = 1
+ url = http://snpeff.sourceforge.net/
+ arch = any
+ license = LGPLv3
+ depends = java-runtime>=8
+ provides = snpeff
+ conflicts = snpeff
+ source = http://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip
+ source = snpeff
+ source = snpsift
+ md5sums = 1fa84a703580a423e27f1e14a945901c
+ md5sums = 9f0415d2e713f0acffec4d88253e769d
+ md5sums = 3a2f8a17dfffca77375806d2dee12b0c
+
+pkgname = snpeff
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 00000000000..80b1be6c53c
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,33 @@
+# Maintainer: Clint Valentine <valentine.clint@gmail.com>
+
+pkgname=snpeff
+pkgver=4_3t
+pkgrel=1
+pkgdesc="Genetic variant annotation and effect prediction toolbox"
+arch=('any')
+url="http://snpeff.sourceforge.net/"
+license=('LGPLv3')
+depends=('java-runtime>=8')
+provides=('snpeff')
+conflicts=('snpeff')
+source=(
+ "http://sourceforge.net/projects/${pkgname}/files/snpEff_v${pkgver}_core.zip"
+ "snpeff"
+ "snpsift"
+)
+md5sums=(
+ '1fa84a703580a423e27f1e14a945901c'
+ '9f0415d2e713f0acffec4d88253e769d'
+ '3a2f8a17dfffca77375806d2dee12b0c'
+)
+
+package() {
+ cd "${srcdir}/"
+
+ install -Dm644 "snpEff/snpEff.jar" "${pkgdir}/usr/share/java/snpEff_v${pkgver}/snpEff.jar"
+ install -Dm644 "snpEff/SnpSift.jar" "${pkgdir}/usr/share/java/snpEff_v${pkgver}/SnpSift.jar"
+ install -Dm644 "snpEff/snpEff.config" "${pkgdir}/usr/share/java/snpEff_v${pkgver}/snpEff.config"
+
+ install -Dm755 "snpeff" "${pkgdir}/usr/bin/snpEff"
+ install -Dm755 "snpsift" "${pkgdir}/usr/bin/SnpSift"
+}
diff --git a/snpeff b/snpeff
new file mode 100644
index 00000000000..1d0f788d416
--- /dev/null
+++ b/snpeff
@@ -0,0 +1,2 @@
+#!/usr/bin/sh
+exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/snpEff.jar' "${@}"
diff --git a/snpsift b/snpsift
new file mode 100644
index 00000000000..32b26dd7263
--- /dev/null
+++ b/snpsift
@@ -0,0 +1,2 @@
+#!/usr/bin/sh
+exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/SnpSift.jar' "${@}"