diff options
| -rw-r--r-- | .SRCINFO | 38 | ||||
| -rw-r--r-- | PKGBUILD | 86 | ||||
| -rwxr-xr-x | snpEff.sh | 2 | ||||
| -rwxr-xr-x | snpSift.sh | 2 | ||||
| -rw-r--r-- | snpeff | 2 | ||||
| -rw-r--r-- | snpsift | 2 |
6 files changed, 86 insertions, 46 deletions
@@ -1,19 +1,27 @@ pkgbase = snpeff - pkgdesc = Genetic variant annotation and effect prediction toolbox - pkgver = 4_3t - pkgrel = 1 - url = http://snpeff.sourceforge.net/ + pkgdesc = Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695 + pkgver = 5.2 + pkgrel = 2 + url = https://pcingola.github.io/SnpEff/ 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 + license = MIT + makedepends = maven + makedepends = java-environment>=12 + makedepends = git + depends = java-runtime>=12 + depends = python + depends = perl + depends = antlr4 + provides = SnpSift + source = SnpEff-5.2.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 = df0cdb4ddde60491789494a809e8fb28a7b6c5f1b18c1f639a76828a4d2c19d27d019cb0b2362c5fa8734c21b770377b8eec6e8beb76fda287e4eda016f380e7 + sha512sums = 074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950 + sha512sums = eb802167761ea7de0b7fdb60b0cc9440d40ea21fe6ed164dc900452e224d71039a8e187e1b7a6499b91338580378c33aa678a23b81f3e27f0f939a4cd3ef6a0c + sha512sums = 9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d + sha512sums = 0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a pkgname = snpeff - @@ -1,33 +1,65 @@ -# Maintainer: Clint Valentine <valentine.clint@gmail.com> - +# Maintainer: Bipin Kumar <kbipinkumar@pm.me> +# Previous Maintainer: Clint Valentine <valentine.clint@gmail.com> pkgname=snpeff -pkgver=4_3t -pkgrel=1 -pkgdesc="Genetic variant annotation and effect prediction toolbox" +_pkgname=SnpEff +_pkg2=SnpSift +pkgver=5.2 +_pkgver2=5.1 +pkgrel=2 +pkgdesc="Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695" 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' -) +url="https://pcingola.github.io/SnpEff/" +provides=('SnpSift') +license=('MIT') +depends=('java-runtime>=12' 'python' 'perl' 'antlr4') +makedepends=('maven' 'java-environment>=12' 'git') +source=("$_pkgname-$pkgver.tar.gz::https://github.com/pcingola/SnpEff/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=('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 +} -package() { - cd "${srcdir}/" +build() { + # Build SnpEff + cd "${srcdir}/$_pkgname-$pkgver" + mvn -e clean compile assembly:single jar:jar + + # Install SnpEff.jar file in local Maven repo as dependency for building SnpSift + mvn install:install-file \ + -Dfile=target/SnpEff-$pkgver.jar \ + -DgroupId=org.snpeff \ + -DartifactId=SnpEff \ + -Dversion=$pkgver \ + -Dpackaging=jar \ + -DgeneratePom=true \ + --quiet - 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" + # Build SnpSift + cd "${srcdir}/$_pkg2-${_pkgver2}" + mvn -e clean compile assembly:single jar:jar + +} - install -Dm755 "snpeff" "${pkgdir}/usr/bin/snpEff" - install -Dm755 "snpsift" "${pkgdir}/usr/bin/SnpSift" +package() { + install -Dm644 ${srcdir}/$_pkgname-$pkgver/target/SnpEff-$pkgver-jar-with-dependencies.jar "${pkgdir}"/usr/share/java/snpEff/snpEff.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 + install -Dm755 snpSift.sh "${pkgdir}"/usr/bin/snpsift } diff --git a/snpEff.sh b/snpEff.sh new file mode 100755 index 000000000000..77ec34448d09 --- /dev/null +++ b/snpEff.sh @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff/snpEff.jar' "${@}"
\ No newline at end of file diff --git a/snpSift.sh b/snpSift.sh new file mode 100755 index 000000000000..f378dc764ee9 --- /dev/null +++ b/snpSift.sh @@ -0,0 +1,2 @@ +#!/usr/bin/sh +exec /usr/bin/java -jar '/usr/share/java/snpEff/snpSift.jar' "${@}"
\ No newline at end of file diff --git a/snpeff b/snpeff deleted file mode 100644 index 1d0f788d4169..000000000000 --- a/snpeff +++ /dev/null @@ -1,2 +0,0 @@ -#!/usr/bin/sh -exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/snpEff.jar' "${@}" 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' "${@}" |