summarylogtreecommitdiffstats
diff options
context:
space:
mode:
-rw-r--r--.SRCINFO16
-rw-r--r--PKGBUILD31
-rw-r--r--SnpSift.sh2
-rw-r--r--snpEff.sh2
-rw-r--r--snpeff2
-rw-r--r--snpsift2
6 files changed, 25 insertions, 30 deletions
diff --git a/.SRCINFO b/.SRCINFO
index 56c0a4e76af..04a778d91cc 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -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
diff --git a/PKGBUILD b/PKGBUILD
index 80b1be6c53c..fd15d348f69 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -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 00000000000..e72def2cfee
--- /dev/null
+++ b/SnpSift.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/sh
+exec /usr/bin/java -jar '/usr/share/java/snpEff/SnpSift.jar' "${@}"
diff --git a/snpEff.sh b/snpEff.sh
new file mode 100644
index 00000000000..16908516028
--- /dev/null
+++ b/snpEff.sh
@@ -0,0 +1,2 @@
+#!/usr/bin/sh
+exec /usr/bin/java -jar '/usr/share/java/snpEff/snpEff.jar' "${@}"
diff --git a/snpeff b/snpeff
deleted file mode 100644
index 1d0f788d416..00000000000
--- a/snpeff
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/sh
-exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/snpEff.jar' "${@}"
diff --git a/snpsift b/snpsift
deleted file mode 100644
index 32b26dd7263..00000000000
--- a/snpsift
+++ /dev/null
@@ -1,2 +0,0 @@
-#!/usr/bin/sh
-exec /usr/bin/java -jar '/usr/share/java/snpEff_v4_3t/SnpSift.jar' "${@}"