New upstream version

(Portage version: 2.1.1-r1)

3 files changed, 211 insertions, 1 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 41c07449a778..c9788936aa7a 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.48 2006/10/30 19:49:22 opfer Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.49 2006/11/03 02:04:56 ribosome Exp $
+
+*ncbi-tools-20061015 (03 Nov 2006)
+
+  03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
+  +ncbi-tools-20061015.ebuild:
+  New upstream version.
 
   30 Oct 2006; Christian Faulhammer <opfer@gentoo.org>
   ncbi-tools-20060507.ebuild:
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015
new file mode 100644
index 000000000000..21bbf17addbb
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015
@@ -0,0 +1,9 @@
+MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
+RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
+SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
+MD5 8eca84753fd7a1d39bab256a4944f65e ncbi-tools-20061015.tar.gz 15772715
+RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 ncbi-tools-20061015.tar.gz 15772715
+SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de ncbi-tools-20061015.tar.gz 15772715
+MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
+RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b ncbi-tools-sdk-doc.tar.bz2 263568
+SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2 ncbi-tools-sdk-doc.tar.bz2 263568
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild
new file mode 100644
index 000000000000..9929a10dd286
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild,v 1.1 2006/11/03 02:04:56 ribosome Exp $
+
+inherit flag-o-matic toolchain-funcs eutils autotools
+
+DESCRIPTION="Development toolkit and applications for computational biology"
+LICENSE="public-domain"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+SRC_URI="mirror://gentoo/${P}.tar.gz
+	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )
+	mpi? ( mirror://gentoo/mpiblast-20060625.tar.gz )"
+
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
+IUSE="doc mpi X"
+
+DEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	sys-devel/pmake
+	mpi? ( virtual/mpi )
+	X? ( virtual/motif )"
+
+S="${WORKDIR}/ncbi"
+
+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_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${PN}-asn2all.patch
+
+	if use ppc64; then
+		epatch "${FILESDIR}"/${PN}-lop.patch
+	fi
+
+	if use mpi; then
+		cd "${WORKDIR}"
+		epatch "${WORKDIR}"/mpiblast/ncbi_Dec2005_evalue.patch
+	fi
+
+	if ! use X; then
+		cd "${S}"/make
+		sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
+			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
+			-i makedis.csh || die
+	else
+		if use x86; then
+			# X applications segfault on startup on x86 with -O3.
+			replace-flags '-O3' '-O2'
+		fi
+	fi
+
+	# Apply user C flags...
+	cd "${S}"/platform
+	# ... on x86...
+	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-i linux-x86.ncbi.mk || die
+	# ... on alpha...
+	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \
+		-i linux-alpha.ncbi.mk || die
+	# ... on hppa...
+	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-i hppalinux.ncbi.mk || die
+	# ... on ppc...
+	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-i ppclinux.ncbi.mk || die
+	# ... on generic Linux.
+	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
+		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
+		-i linux.ncbi.mk || die
+
+	# Put in our MAKEOPTS (doesn't work).
+	# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh
+
+	# Set C compiler...
+	# ... on x86...
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die
+	# ... on alpha...
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die
+	# ... on hppa...
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die
+	# ... on ppc...
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die
+	# ... on generic Linux.
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
+
+	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
+	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
+	cd "${S}"/make
+	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
+			"Failed to replace make by pmake."
+}
+
+src_compile() {
+	cd "${WORKDIR}"
+	ncbi/make/makedis.csh || die
+	mkdir "${S}"/cgi
+	mkdir "${S}"/real
+	mv "${S}"/bin/*.cgi "${S}"/cgi || die
+	mv "${S}"/bin/*.REAL "${S}"/real || die
+
+	if use mpi; then
+		cd "${WORKDIR}"/mpiblast
+		AM_OPT="-a"
+		eautoreconf
+		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die
+		emake || die
+	fi
+}
+
+src_install() {
+	dobin "${S}"/bin/* || die "Failed to install binaries."
+	dobin "${S}"/build/asn2all || die "Failed to install binaries."
+	dolib "${S}"/lib/* || die "Failed to install libraries."
+	mkdir -p "${D}"/usr/include/ncbi
+	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
+		die "Failed to install headers."
+
+	if use mpi; then
+		cd "${WORKDIR}"/mpiblast
+		make install DESTDIR="${D}" || die "Failed to install MPI blast."
+	fi
+
+	# TODO: Web apps
+	#insinto /usr/share/ncbi/lib/cgi
+	#doins ${S}/cgi/*
+	#insinto /usr/share/ncbi/lib/real
+	#doins ${S}/real/*
+	# TODO: Add support for wwwblast.
+
+	# Basic documentation
+	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
+		die "Failed to install basic documentation."
+	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
+		die "Failed renaming fa2htgs documentation."
+	newdoc "${S}"/config/README README.config || \
+		die "Failed renaming config documentation."
+	newdoc "${S}"/network/encrypt/README README.encrypt || \
+		die "Failed renaming encrypt documentation."
+	newdoc "${S}"/network/nsclilib/readme README.nsclilib || \
+	die "Failed renaming nsclilib documentation."
+	newdoc "${S}"/sequin/README README.sequin || \
+		die "Failed renaming sequin documentation."
+	doman "${S}"/doc/man/* || \
+		die "Failed to install man pages."
+
+	# Hypertext user documentation
+	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
+		die "Failed to install HTML documentation."
+	insinto /usr/share/doc/${PF}/html/blast
+	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
+
+	# Developer documentation
+	if use doc; then
+		# Hypertext SDK documentation
+		insinto /usr/share/doc/${PF}/html/sdk
+		doins "${WORKDIR}"/${PN}-sdk-doc/* || die
+
+		# Demo programs
+		mkdir "${D}"/usr/share/ncbi
+		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
+	fi
+
+	# Shared data (similarity matrices and such) and database directory.
+	insinto /usr/share/ncbi/data
+	doins "${S}"/data/* || die "Failed to install shared data."
+	dodir /usr/share/ncbi/formatdb || die
+
+	# Default config file to set the path for shared data.
+	insinto /etc/ncbi
+	newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
+
+	# Env file to set the location of the config file and BLAST databases.
+	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
+}