sci-biology/ncbi-tools: Version BUmp, #416251; restructured large parts of the ebuild; move to EAPI=4

(Portage version: 2.2.0_alpha107/cvs/Linux x86_64)

2 files changed, 155 insertions, 1 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 5ac1d01e4842..e274e46a652b 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.83 2012/04/26 16:08:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.84 2012/05/22 18:32:11 jlec Exp $
+
+*ncbi-tools-2.2.26 (22 May 2012)
+
+  22 May 2012; Justin Lecher <jlec@gentoo.org> +ncbi-tools-2.2.26.ebuild:
+  Version BUmp, #416251; restructured large parts of the ebuild; move to EAPI=4
 
   26 Apr 2012; Justin Lecher <jlec@gentoo.org> ncbi-tools-20080302.ebuild,
   -ncbi-tools-20090809-r2.ebuild:
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
new file mode 100644
index 000000000000..14796d03e268
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
@@ -0,0 +1,149 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild,v 1.1 2012/05/22 18:32:11 jlec Exp $
+
+EAPI=4
+
+inherit flag-o-matic toolchain-funcs eutils
+
+DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="public-domain"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc static-libs X"
+
+RDEPEND="
+	app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	X? ( x11-libs/openmotif:0 )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/ncbi"
+
+EXTRA_VIB="asn2all asn2asn"
+
+pkg_setup() {
+	echo
+	ewarn 'Please note that the NCBI toolkit (and especially the X'
+	ewarn 'applications) are known to have compilation and run-time'
+	ewarn 'problems when compiled with agressive compilation flags. The'
+	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
+	ewarn 'X support is enabled.'
+	echo
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-extra_vib.patch
+
+	if use ppc || use ppc64; then
+		epatch "${FILESDIR}"/${PN}-lop.patch
+	fi
+
+	if ! use X; then
+		sed \
+			-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
+			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
+			-i "${S}"/make/makedis.csh || die
+	else
+		# X applications segfault on startup on x86 with -O3.
+		use x86 || replace-flags '-O3' '-O2'
+	fi
+
+	# Apply user C flags...
+	cd "${S}"/platform
+	sed \
+		-e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" \
+		-e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS} ${LDFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-i linux-x86.ncbi.mk linux-alpha.ncbi.mk hppalinux.ncbi.mk \
+			ppclinux.ncbi.mk linux64.ncbi.mk linux.ncbi.mk || die
+
+	# We use dynamic libraries
+	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
+
+	sed \
+		-re "s:/usr(/bin/.*sh):\1:g" \
+		-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
+		-i $(find "${S}" -type f) || die
+}
+
+src_compile() {
+	export EXTRA_VIB
+	cd "${WORKDIR}"
+	csh ncbi/make/makedis.csh || die
+	mkdir "${S}"/cgi "${S}"/real || die
+	mv "${S}"/bin/*.cgi "${S}"/cgi || die
+	mv "${S}"/bin/*.REAL "${S}"/real || die
+	cd "${S}"/demo
+	emake \
+		-f ../make/makenet.unx \
+		CC="$(tc-getCC) ${CFLAGS} -I../include  -L../lib" \
+		LDFLAGS="${LDFLAGS}" \
+		spidey
+	cp spidey ../bin/ || die
+}
+
+src_install() {
+	#sci-geosciences/cdat-lite
+	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
+
+	dobin "${S}"/bin/*
+
+	for i in ${EXTRA_VIB}; do
+		dobin "${S}"/build/${i} || die "Failed to install binaries."
+	done
+	use static-libs && dolib.a "${S}"/lib/*.a
+	mkdir -p "${ED}"/usr/include/ncbi
+	cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
+		die "Failed to install headers."
+
+	# TODO: wwwblast with webapps
+	#insinto /usr/share/ncbi/lib/cgi
+	#doins ${S}/cgi/*
+	#insinto /usr/share/ncbi/lib/real
+	#doins ${S}/real/*
+
+	# Basic documentation
+	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}}
+	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs
+	newdoc "${S}"/config/README README.config
+	newdoc "${S}"/network/encrypt/README README.encrypt
+	newdoc "${S}"/network/nsclilib/readme README.nsclilib
+	newdoc "${S}"/sequin/README README.sequin
+	doman "${S}"/doc/man/*
+
+	# Hypertext user documentation
+	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
+	insinto /usr/share/doc/${PF}/html
+	doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
+
+	# Developer documentation
+	if use doc; then
+		# Demo programs
+		mkdir "${ED}"/usr/share/ncbi
+		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
+	fi
+
+	# Shared data (similarity matrices and such) and database directory.
+	insinto /usr/share/ncbi
+	doins -r "${S}"/data
+	dodir /usr/share/ncbi/formatdb
+
+	# Default config file to set the path for shared data.
+	insinto /etc/ncbi
+	newins "${FILESDIR}"/ncbirc .ncbirc
+
+	# Env file to set the location of the config file and BLAST databases.
+	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
+}