diff options
| -rw-r--r-- | .SRCINFO | 16 | ||||
| -rw-r--r-- | PKGBUILD | 31 | ||||
| -rw-r--r-- | SnpSift.sh | 2 | ||||
| -rw-r--r-- | snpEff.sh | 2 | ||||
| -rw-r--r-- | snpeff | 2 | ||||
| -rw-r--r-- | snpsift | 2 |
6 files changed, 25 insertions, 30 deletions
@@ -1,19 +1,17 @@ pkgbase = snpeff pkgdesc = Genetic variant annotation and effect prediction toolbox pkgver = 4_3t - pkgrel = 1 + pkgrel = 2 url = http://snpeff.sourceforge.net/ arch = any - license = LGPLv3 + license = (L)GPL3 depends = java-runtime>=8 - provides = snpeff - conflicts = snpeff + source = snpEff.sh + source = SnpSift.sh source = http://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip - source = snpeff - source = snpsift - md5sums = 1fa84a703580a423e27f1e14a945901c - md5sums = 9f0415d2e713f0acffec4d88253e769d - md5sums = 3a2f8a17dfffca77375806d2dee12b0c + sha256sums = e0ba5679a90efdb39cd9398b1db708444fd8e5321182cedf72696b3ae1e2e2b9 + sha256sums = 4bd0163c6b8864ed6ea3f20d215b0bf371e10eaa4156ffcf8429d6f71ded93e3 + sha256sums = d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244 pkgname = snpeff @@ -2,32 +2,29 @@ pkgname=snpeff pkgver=4_3t -pkgrel=1 +pkgrel=2 pkgdesc="Genetic variant annotation and effect prediction toolbox" arch=('any') url="http://snpeff.sourceforge.net/" -license=('LGPLv3') +license=('(L)GPL3') depends=('java-runtime>=8') -provides=('snpeff') -conflicts=('snpeff') source=( - "http://sourceforge.net/projects/${pkgname}/files/snpEff_v${pkgver}_core.zip" - "snpeff" - "snpsift" + snpEff.sh + SnpSift.sh + http://sourceforge.net/projects/"${pkgname}"/files/snpEff_v"${pkgver}"_core.zip ) -md5sums=( - '1fa84a703580a423e27f1e14a945901c' - '9f0415d2e713f0acffec4d88253e769d' - '3a2f8a17dfffca77375806d2dee12b0c' +sha256sums=( + 'e0ba5679a90efdb39cd9398b1db708444fd8e5321182cedf72696b3ae1e2e2b9' + '4bd0163c6b8864ed6ea3f20d215b0bf371e10eaa4156ffcf8429d6f71ded93e3' + 'd55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244' ) 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" "${pkgdir}/usr/bin/SnpSift" + install -Dm644 snpEff/snpEff.jar "${pkgdir}"/usr/share/java/snpEff/snpEff.jar + install -Dm644 snpEff/SnpSift.jar "${pkgdir}"/usr/share/java/snpEff/SnpSift.jar + install -Dm644 snpEff/snpEff.config "${pkgdir}"/usr/share/java/snpEff/snpEff.config + install -Dm755 snpEff.sh "${pkgdir}"/usr/bin/snpEff + install -Dm755 SnpSift.sh "${pkgdir}"/usr/bin/SnpSift } diff --git a/SnpSift.sh b/SnpSift.sh new file mode 100644 index 000000000000..e72def2cfee1 --- /dev/null +++ b/SnpSift.sh @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff/SnpSift.jar' "${@}" diff --git a/snpEff.sh b/snpEff.sh new file mode 100644 index 000000000000..169085160289 --- /dev/null +++ b/snpEff.sh @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff/snpEff.jar' "${@}" diff --git a/snpeff b/snpeff deleted file mode 100644 index 1d0f788d4169..000000000000 --- a/snpeff +++ /dev/null @@ -1,2 +0,0 @@ -#!/usr/bin/sh -exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/snpEff.jar' "${@}" diff --git a/snpsift b/snpsift deleted file mode 100644 index 32b26dd72633..000000000000 --- a/snpsift +++ /dev/null @@ -1,2 +0,0 @@ -#!/usr/bin/sh -exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/SnpSift.jar' "${@}" |