Import from Science overlay

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 109 insertions, 0 deletions

diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog
new file mode 100644
index 000000000000..dd17eec89d20
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-biology/ncbi-tools++
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ChangeLog,v 1.1 2009/07/27 05:26:29 weaver Exp $
+
+*ncbi-tools++-2009.05.15 (27 Jul 2009)
+
+  27 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
+  +ncbi-tools++-2009.05.15.ebuild:
+  Import from Science overlay
+
+  25 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  Version bump
+
+  28 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog:
+  New package, ebuild written by me
+
diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest
new file mode 100644
index 000000000000..883a7fccf932
--- /dev/null
+++ b/sci-biology/ncbi-tools++/Manifest
@@ -0,0 +1,4 @@
+DIST ncbi_cxx--May_15_2009.tar.gz 13986626 RMD160 131a04d43056fd4d4fd1781d38a5c1b9e3089a13 SHA1 0cecad93774ce40b3455149b2c3538dfce032b85 SHA256 ccb86f2e33251580e23c94b8d2a4aa4832c278171ded29513f0c9859b303f1d8
+EBUILD ncbi-tools++-2009.05.15.ebuild 1996 RMD160 5248a055b9c314de554dd7f4ec94be47b78ff6d4 SHA1 527bda28e4fd74558fc82f2c6089152dd016044d SHA256 f44c1a101d2a79e95b201caf666e02be676afd985680e6bed0fd97ed8517d954
+MISC ChangeLog 567 RMD160 c87420983e60846725511e46237f6df914d2ec36 SHA1 463ab01d880f9d409cc7d0091a0ef26271d6cba3 SHA256 2ead81b240980210baffbe956481bfc9ce39118fcabb3bf212af1b990926af73
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/ncbi-tools++/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15.ebuild
new file mode 100644
index 000000000000..5cdc3afb8362
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools++/ncbi-tools++-2009.05.15.ebuild,v 1.1 2009/07/27 05:26:29 weaver Exp $
+
+EAPI="2"
+
+inherit multilib
+
+MY_TAG="May_15_2009"
+MY_Y="${TAG/*_/}"
+MY_P="ncbi_cxx--${MY_TAG}"
+
+DESCRIPTION="NCBI C++ Toolkit"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
+SRC_URI="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/${MY_Y}/${MY_TAG}/${MY_P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+#IUSE="X unicode opengl gnutls test"
+IUSE="sqlite"
+KEYWORDS="~amd64 ~x86"
+
+# wxGTK: must run eselect wxwindows after installing wxgtk or build will fail. Check and abort here.
+# dev-libs/xalan-c - problems detecting, api mismatch?
+
+# apparently gbench-only dependencies
+#	dev-libs/libxml2
+#	dev-libs/libxslt
+#	dev-libs/xerces-c
+#	dev-libs/lzo:2
+#	dev-libs/boost
+#	app-text/sablotron
+#	media-libs/libpng
+#	media-libs/tiff
+#	media-libs/jpeg
+#	x11-libs/libXpm
+#	unicode? ( dev-libs/icu )
+#	opengl? ( media-libs/glut
+#		media-libs/mesa )
+#	gnutls? ( net-libs/gnutls )
+#	X? ( x11-libs/fltk:1.1
+#		x11-libs/wxGTK )
+
+DEPEND="sqlite? ( dev-db/sqlite:3 )"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_configure() {
+	# econf fails
+	"${S}"/configure --without-debug --with-bin-release --prefix="${D}"/usr \
+		--libdir="${D}"/usr/$(get_libdir) \
+		--with-z="/usr" \
+		--with-bz2="/usr" \
+		--with-pcre="/usr" \
+		--with-openssl="/usr" \
+		|| die
+
+# apparently gbench-only configs
+#		--with-boost="/usr" \
+#		--with-sablot="/usr" \
+#		--with-icu="/usr" \
+#		--with-fltk="/usr" \
+#		--with-mesa="/usr" \
+#		--with-glut="/usr" \
+#		--with-wxwidgets="/usr" \
+# problems detecting this
+#		--with-xalan="/usr" \
+}
+
+src_compile() {
+	emake all_r -C GCC*-Release*/build || die
+}
+
+src_install() {
+	emake install || die
+	# File collisions with sci-biology/ncbi-tools
+	rm -f "${D}"/usr/bin/{asn2asn,rpsblast,test_regexp}
+	rm -f "${D}"/usr/$(get_libdir)/libblast.a
+}