diff options
author | BioArchLinuxBot | 2023-10-03 12:02:46 +0000 |
---|---|---|
committer | BioArchLinuxBot | 2023-10-03 12:02:46 +0000 |
commit | 6136a2cad0f526189539cd6be26f56caafe1585d (patch) | |
tree | 18324d0d9ea7ff8bc6e65f5f0f228a4da05b13af | |
parent | 73c222c87c876ac0670b6afc062610b0d1ade574 (diff) | |
download | aur-snpeff.tar.gz |
[lilac] updated to 5.2-2
-rw-r--r-- | .SRCINFO | 11 | ||||
-rw-r--r-- | PKGBUILD | 27 |
2 files changed, 27 insertions, 11 deletions
@@ -1,23 +1,26 @@ pkgbase = snpeff pkgdesc = Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695 - pkgver = 5.1 - pkgrel = 3 + pkgver = 5.2 + pkgrel = 2 url = https://pcingola.github.io/SnpEff/ arch = any license = MIT makedepends = maven makedepends = java-environment>=12 + makedepends = git depends = java-runtime>=12 depends = python depends = perl depends = antlr4 provides = SnpSift - source = SnpEff-5.1.tar.gz::https://github.com/pcingola/SnpEff/archive/refs/tags/v5.1.tar.gz + source = SnpEff-5.2.tar.gz::https://github.com/pcingola/SnpEff/archive/refs/tags/v5.2.tar.gz source = SnpSift-5.1.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v5.1.tar.gz + source = https.patch::https://patch-diff.githubusercontent.com/raw/pcingola/SnpSift/pull/84.patch source = snpSift.sh source = snpEff.sh - sha512sums = eb12a126f71536eb04132e40b5f3e0bea33b6512dce999a70e5c170d2839d739ea8b52e5b38822e83c544693aec7ece20f13674634ae3971a6f08659dc7b9640 + sha512sums = df0cdb4ddde60491789494a809e8fb28a7b6c5f1b18c1f639a76828a4d2c19d27d019cb0b2362c5fa8734c21b770377b8eec6e8beb76fda287e4eda016f380e7 sha512sums = 074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950 + sha512sums = eb802167761ea7de0b7fdb60b0cc9440d40ea21fe6ed164dc900452e224d71039a8e187e1b7a6499b91338580378c33aa678a23b81f3e27f0f939a4cd3ef6a0c sha512sums = 9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d sha512sums = 0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a @@ -3,24 +3,37 @@ pkgname=snpeff _pkgname=SnpEff _pkg2=SnpSift -pkgver=5.1 -pkgrel=3 +pkgver=5.2 +_pkgver2=5.1 +pkgrel=2 pkgdesc="Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695" arch=('any') url="https://pcingola.github.io/SnpEff/" provides=('SnpSift') license=('MIT') depends=('java-runtime>=12' 'python' 'perl' 'antlr4') -makedepends=('maven' 'java-environment>=12') +makedepends=('maven' 'java-environment>=12' 'git') source=("$_pkgname-$pkgver.tar.gz::https://github.com/pcingola/SnpEff/archive/refs/tags/v$pkgver.tar.gz" - "$_pkg2-$pkgver.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v$pkgver.tar.gz" + "$_pkg2-${_pkgver2}.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v${_pkgver2}.tar.gz" + "https.patch::https://patch-diff.githubusercontent.com/raw/pcingola/SnpSift/pull/84.patch" "snpSift.sh" "snpEff.sh" ) -sha512sums=('eb12a126f71536eb04132e40b5f3e0bea33b6512dce999a70e5c170d2839d739ea8b52e5b38822e83c544693aec7ece20f13674634ae3971a6f08659dc7b9640' +sha512sums=('df0cdb4ddde60491789494a809e8fb28a7b6c5f1b18c1f639a76828a4d2c19d27d019cb0b2362c5fa8734c21b770377b8eec6e8beb76fda287e4eda016f380e7' '074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950' + 'eb802167761ea7de0b7fdb60b0cc9440d40ea21fe6ed164dc900452e224d71039a8e187e1b7a6499b91338580378c33aa678a23b81f3e27f0f939a4cd3ef6a0c' '9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d' '0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a') +prepare() { + # fix pom.xml of SnpSift + cd "${srcdir}/$_pkg2-${_pkgver2}" + # fix http sources for dependencies + patch -p1 < ${srcdir}/https.patch + # set correct snpeff version as dependency + export snpver=$(sed -n '41p' pom.xml | cut -d '>' -f 2 | cut -d '<' -f 1) + sed -i "41s/${snpver}/[${pkgver},)/g" pom.xml +} + build() { # Build SnpEff cd "${srcdir}/$_pkgname-$pkgver" @@ -37,14 +50,14 @@ build() { --quiet # Build SnpSift - cd "${srcdir}/$_pkg2-$pkgver" + cd "${srcdir}/$_pkg2-${_pkgver2}" mvn -e clean compile assembly:single jar:jar } package() { install -Dm644 ${srcdir}/$_pkgname-$pkgver/target/SnpEff-$pkgver-jar-with-dependencies.jar "${pkgdir}"/usr/share/java/snpEff/snpEff.jar - install -Dm644 ${srcdir}/$_pkg2-$pkgver/target/SnpSift-$pkgver-jar-with-dependencies.jar "${pkgdir}"/usr/share/java/snpEff/snpSift.jar + install -Dm644 ${srcdir}/$_pkg2-${_pkgver2}/target/SnpSift-${_pkgver2}-jar-with-dependencies.jar "${pkgdir}"/usr/share/java/snpEff/snpSift.jar install -Dm644 ${srcdir}/$_pkgname-$pkgver/config/snpEff.config "${pkgdir}"/usr/share/java/snpEff/snpEff.config install -Dm644 ${srcdir}/$_pkgname-$pkgver/LICENSE.md "${pkgdir}"/usr/share/licenses/$pkgname/LICENSE install -Dm755 snpEff.sh "${pkgdir}"/usr/bin/snpeff |