diff options
| -rw-r--r-- | .SRCINFO | 19 | ||||
| -rw-r--r-- | PKGBUILD | 33 | ||||
| -rw-r--r-- | snpeff | 2 | ||||
| -rw-r--r-- | snpsift | 2 |
4 files changed, 56 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..56c0a4e76afc --- /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 000000000000..80b1be6c53cf --- /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" "${pkgdir}/usr/bin/SnpSift" +} diff --git a/snpeff b/snpeff new file mode 100644 index 000000000000..1d0f788d4169 --- /dev/null +++ b/snpeff @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/snpEff.jar' "${@}" diff --git a/snpsift b/snpsift new file mode 100644 index 000000000000..32b26dd72633 --- /dev/null +++ b/snpsift @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/SnpSift.jar' "${@}" |