sci-biology/staden-2.0.0_beta8: new release

(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)

1 files changed, 68 insertions, 0 deletions

diff --git a/sci-biology/staden/staden-2.0.0_beta8.ebuild b/sci-biology/staden/staden-2.0.0_beta8.ebuild
new file mode 100644
index 000000000..a79bfd2fc
--- /dev/null
+++ b/sci-biology/staden/staden-2.0.0_beta8.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils flag-o-matic base
+
+DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)."
+HOMEPAGE="http://sourceforge.net/projects/staden"
+SRC_URI="http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz
+		http://sourceforge.net/projects/staden/files/staden/2.0.0b8/staden_doc-2.0.0b8-src.tar.gz"
+
+LICENSE="staden"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="debug fortran X png curl tcl tk zlib"
+
+# either g77 or gfortran must be available
+# edit src/mk/linux.mk accordingly
+
+#
+# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
+#
+# 
+#
+DEPEND=">=dev-lang/tk-8.4
+		>=dev-lang/tcl-8.4
+		dev-tcltk/tklib
+		>=sci-libs/io_lib-1.12.2
+		>=sys-libs/zlib-1.2
+		>=media-libs/libpng-1.2
+		sci-biology/samtools
+		>=app-arch/xz-utils-4.999"
+
+# maybe we should depend on app-arch/lzma or app-arch/xz-utils?
+
+RDEPEND="tcl? ( >=dev-tcltk/itcl-3.2 )
+		tk? ( >=dev-tcltk/itk-3.2 )
+		>=dev-tcltk/iwidgets-4.0"
+
+S="${WORKDIR}"/staden-2.0.0b8-src
+
+src_prepare() {
+	unpack ${A} || die
+	cd "${S}" || die "Cannot cd ${WORKDIR}/staden-2.0.0b8-src"
+	epatch "${FILESDIR}"/rpath.patch || die "failed to apply -rpath=/usr/lib/staden patch"
+	./bootstrap || die "bootstrap failed"
+}
+
+src_configure(){
+	local myconf
+	use X && myconf=" --with-x"
+	myconf=" --with-tklib=/usr/lib/tklib0.5" # HACK
+	use amd64 && myconf="${myconf} --enable-64bit"
+	use debug && append-cflags "-DCACHE_REF_DEBUG"
+	econf ${myconf} || die "configure failed"
+}
+
+src_compile() {
+	emake || die "emake failed"
+}
+
+src_install() {
+	emake install DESTDIR="${D}" || die "make install failed"
+	#cd "${WORKDIR}"/staden_doc-2.0.0b8-src || die "failed to cd "${WORKDIR}"/staden_doc-2.0.0b8-src"
+	#make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
+}