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authorBioArchLinuxBot2023-10-03 12:02:46 +0000
committerBioArchLinuxBot2023-10-03 12:02:46 +0000
commit6136a2cad0f526189539cd6be26f56caafe1585d (patch)
tree18324d0d9ea7ff8bc6e65f5f0f228a4da05b13af
parent73c222c87c876ac0670b6afc062610b0d1ade574 (diff)
downloadaur-snpeff.tar.gz
[lilac] updated to 5.2-2
-rw-r--r--.SRCINFO11
-rw-r--r--PKGBUILD27
2 files changed, 27 insertions, 11 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 01b7951277b4..94d396d8fdf6 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -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
diff --git a/PKGBUILD b/PKGBUILD
index 20ca51e69c97..70bca520869f 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -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