proovread-2.12-1

2 files changed, 55 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..2cb6a6669c5e
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,17 @@
+pkgbase = proovread
+	pkgdesc = large-scale high accuracy PacBio correction through iterative short read consensus
+	pkgver = 2.12
+	pkgrel = 1
+	url = https://github.com/BioInf-Wuerzburg/proovread
+	arch = any
+	license = PerlArtistic
+	depends = blasr-git
+	depends = perl-log-log4perl
+	depends = blast+>=2.2.24
+	depends = samtools>=1.1
+	depends = shrimp
+	source = proovread::git+https://github.com/BioInf-Wuerzburg/proovread#tag=proovread-2.12
+	md5sums = SKIP
+
+pkgname = proovread
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..93f5f1047980
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,38 @@
+# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=proovread
+pkgver=2.12
+pkgrel=1
+pkgdesc="large-scale high accuracy PacBio correction through iterative short read consensus"
+arch=('any')
+url="https://github.com/BioInf-Wuerzburg/proovread"
+license=('PerlArtistic')
+depends=('blasr-git' 'perl-log-log4perl' 'blast+>=2.2.24' 'samtools>=1.1' 'shrimp')
+source=("$pkgname::git+https://github.com/BioInf-Wuerzburg/proovread#tag=proovread-2.12")
+md5sums=('SKIP')
+
+prepare() {
+  cd $srcdir/$pkgname
+
+  git submodule init
+  git submodule update
+}
+
+build() {
+  cd $srcdir/$pkgname/util/bwa
+
+  make
+}
+
+package() {
+  cd $srcdir/$pkgname
+
+  mkdir -p $pkgdir/usr/bin \
+           $pkgdir/usr/lib/perl5/vendor_perl
+
+  for file in bin/* util/SeqChunker/bin/* ; do
+    install -Dm755 $file $pkgdir/usr/bin/$(basename $file .pl)
+  done
+
+  cp -r lib/* $pkgdir/usr/lib/perl5/vendor_perl
+}