[lilac] updated to 5.1-2

5 files changed, 62 insertions, 36 deletions

diff --git a/.SRCINFO b/.SRCINFO
index e24939ab1d16..a5397f1389d2 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,17 +1,24 @@
 pkgbase = snpeff
-	pkgdesc = Genetic variant annotation and effect prediction toolbox. https://doi.org/10.4161/fly.19695
+	pkgdesc = Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695
 	pkgver = 5.1
-	pkgrel = 1
+	pkgrel = 2
 	url = https://pcingola.github.io/SnpEff/
 	arch = any
 	license = MIT
-	depends = java-runtime>=12pythonperlbash
-	provides = snpeff
+	makedepends = maven
+	makedepends = java-environment>=12
+	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 = SnpSift-5.1.tar.gz::https://github.com/pcingola/SnpSift/archive/refs/tags/v5.1.tar.gz
+	source = snpSift.sh
 	source = snpEff.sh
-	source = SnpSift.sh
-	source = https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
-	sha256sums = e0ba5679a90efdb39cd9398b1db708444fd8e5321182cedf72696b3ae1e2e2b9
-	sha256sums = 4bd0163c6b8864ed6ea3f20d215b0bf371e10eaa4156ffcf8429d6f71ded93e3
-	sha256sums = 919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b
+	sha512sums = eb12a126f71536eb04132e40b5f3e0bea33b6512dce999a70e5c170d2839d739ea8b52e5b38822e83c544693aec7ece20f13674634ae3971a6f08659dc7b9640
+	sha512sums = 074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950
+	sha512sums = 9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d
+	sha512sums = 0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a
 
 pkgname = snpeff
diff --git a/PKGBUILD b/PKGBUILD
index f750294f7d56..4dcb5d93dc04 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,33 +1,52 @@
 # Maintainer: Bipin Kumar <bipin@ccmb.res.in>
-# previous Maintainer: Clint Valentine <valentine.clint@gmail.com>
+# Previous Maintainer: Clint Valentine <valentine.clint@gmail.com>
 pkgname=snpeff
+_pkgname=SnpEff
+_pkg2=SnpSift
 pkgver=5.1
-pkgrel=1
-pkgdesc="Genetic variant annotation and effect prediction toolbox. https://doi.org/10.4161/fly.19695"
+pkgrel=2
+pkgdesc="Genetic variant annotation and effect prediction toolbox. doi:10.4161/fly.19695"
 arch=('any')
 url="https://pcingola.github.io/SnpEff/"
-provides=(""${pkgname%-pkgver}"")
+provides=('SnpSift')
 license=('MIT')
-depends=('java-runtime>=12''python''perl''bash')
-source=(
-  snpEff.sh
-  SnpSift.sh
-  https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
-)
-sha256sums=('e0ba5679a90efdb39cd9398b1db708444fd8e5321182cedf72696b3ae1e2e2b9'
-            '4bd0163c6b8864ed6ea3f20d215b0bf371e10eaa4156ffcf8429d6f71ded93e3'
-            '919e0595c08e86d1dd82279723c83cb872070244ee4ce0cb3167bde2b272893b')
+depends=('java-runtime>=12' 'python' 'perl' 'antlr4')
+makedepends=('maven' 'java-environment>=12')
+source=("$_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$pkgver.tar.gz"
+        "snpSift.sh"
+        "snpEff.sh"
+       )
+sha512sums=('eb12a126f71536eb04132e40b5f3e0bea33b6512dce999a70e5c170d2839d739ea8b52e5b38822e83c544693aec7ece20f13674634ae3971a6f08659dc7b9640'
+            '074139695584227d3e523962b81ed1cd1687a146b973ec761e5c42fccf865b6f01bd8fc1280a1f73e7c9ab3292bfc3358d56a572f0795bd05fa879011a4ad950'
+            '9819376173c372cec8ae3f28d1b3857a1b63690bf16213e6f26ebd5d29150616c8f8a3d0ecf8d9ba24c34e24f28ab56edecf8c9cee3c578ae673da7c65c48f0d'
+            '0eb2339b55969cc065b8c15bee06d8728b0576689217777bf24e209409d61210f91e814bb1a5dddc651dd2a3f35d0f3911bd3161d6d3275604ea58cf83f9086a')
+build() {
+	# Build SnpEff
+    cd "${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
+
+    # Build SnpSift
+    cd "${srcdir}/$_pkg2-$pkgver"
+    mvn -e clean compile assembly:single jar:jar
+    
+}
 
 package() {
-  cd "${srcdir}/"
-  install -Dm644 snpEff/snpEff.jar  "${pkgdir}"/usr/share/java/snpEff/snpEff.jar
-  for d in snpEff/ ; do
-    cp -R "$d" "${pkgdir}"/usr/share/java/
-  done
-  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 "${pkgdir}"/usr/share/java/snpEff/snpEff.config
-  install -Dm644 snpEff/LICENSE.md "${pkgdir}"/usr/share/licenses/snpEff/LICENSE.md
-  install -Dm755 snpEff.sh "${pkgdir}"/usr/bin/snpEff
-  install -Dm755 SnpSift.sh "${pkgdir}"/usr/bin/SnpSift
+    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 ${srcdir}/$_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 "${pkgdir}"/usr/bin/snpsift
 }
diff --git a/SnpSift.sh b/SnpSift.sh
deleted file mode 100644
index e72def2cfee1..000000000000
--- a/SnpSift.sh
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/sh
-exec /usr/bin/java -jar '/usr/share/java/snpEff/SnpSift.jar' "${@}"
diff --git a/snpEff.sh b/snpEff.sh
index 169085160289..77ec34448d09 100644..100755
--- a/snpEff.sh
+++ b/snpEff.sh
@@ -1,2 +1,2 @@
 #!/usr/bin/sh
-exec /usr/bin/java -jar '/usr/share/java/snpEff/snpEff.jar' "${@}"
+exec /usr/bin/java -jar '/usr/share/java/snpEff/snpEff.jar' "${@}"
\ 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