diff options
| author | Christian Krause | 2015-06-13 11:58:15 +0200 |
|---|---|---|
| committer | Christian Krause | 2015-06-13 11:58:15 +0200 |
| commit | f31f39626df0db64c1c873a5bfb8d7ddd6939769 (patch) | |
| tree | 3bd6466f7ed5e63877abfcac53cf6df102345d9b | |
| download | aur-f31f39626df0db64c1c873a5bfb8d7ddd6939769.tar.gz | |
Initial import
| -rw-r--r-- | .SRCINFO | 19 | ||||
| -rw-r--r-- | PKGBUILD | 33 | ||||
| -rw-r--r-- | picard-profile.sh | 1 | ||||
| -rw-r--r-- | picard.sh | 2 |
4 files changed, 55 insertions, 0 deletions
diff --git a/.SRCINFO b/.SRCINFO new file mode 100644 index 000000000000..e2bfada8a0c8 --- /dev/null +++ b/.SRCINFO @@ -0,0 +1,19 @@ +pkgbase = picard-tools + pkgdesc = set of tools for working with next generation sequencing data in the BAM format + pkgver = 1.133 + pkgrel = 1 + url = https://github.com/broadinstitute/picard + arch = i686 + arch = x86_64 + license = GPL2 + depends = bash + depends = java-runtime>=6 + source = https://github.com/broadinstitute/picard/releases/download/1.133/picard-tools-1.133.zip + source = picard-profile.sh + source = picard.sh + md5sums = 93a987e67ce4a05ac68559515a1352f2 + md5sums = ebcda2d2c55df6d05994252cf22a68c2 + md5sums = 0987aa56f62f5e843bfa788cc93626c8 + +pkgname = picard-tools + diff --git a/PKGBUILD b/PKGBUILD new file mode 100644 index 000000000000..70274f11eb3a --- /dev/null +++ b/PKGBUILD @@ -0,0 +1,33 @@ +# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> + +pkgname=picard-tools +pkgver=1.133 +pkgrel=1 +pkgdesc='set of tools for working with next generation sequencing data in the BAM format' +arch=('i686' 'x86_64') +url="https://github.com/broadinstitute/picard" +license=('GPL2') +depends=('bash' 'java-runtime>=6') +source=("https://github.com/broadinstitute/picard/releases/download/$pkgver/$pkgname-$pkgver.zip" + 'picard-profile.sh' + 'picard.sh') +md5sums=('93a987e67ce4a05ac68559515a1352f2' + 'ebcda2d2c55df6d05994252cf22a68c2' + '0987aa56f62f5e843bfa788cc93626c8') + +package() { + cd $srcdir/$pkgname-$pkgver + + for f in *.jar ; do + install -Dm755 $f $pkgdir/usr/share/java/picard-tools/$f + done + + install -Dm755 libIntelDeflater.so $pkgdir/usr/lib/libIntelDeflater.so + + pushd $pkgdir/usr/share/java/picard-tools > /dev/null + ln -s ../../../lib/libIntelDeflater.so + popd > /dev/null + + install -Dm755 $srcdir/picard.sh $pkgdir/usr/bin/picard + install -Dm755 $srcdir/picard-profile.sh $pkgdir/etc/profile.d/picard.sh +} diff --git a/picard-profile.sh b/picard-profile.sh new file mode 100644 index 000000000000..5c314e1a5e5b --- /dev/null +++ b/picard-profile.sh @@ -0,0 +1 @@ +export PICARD_HOME=/usr/share/java/picard-tools diff --git a/picard.sh b/picard.sh new file mode 100644 index 000000000000..dd39af1c1bdb --- /dev/null +++ b/picard.sh @@ -0,0 +1,2 @@ +#!/bin/sh +exec /usr/bin/java $JVM_OPTS -jar /usr/share/java/picard-tools/picard.jar "$@" |