New upstream version

Package-Manager: portage-2.1.1-r1

4 files changed, 223 insertions, 15 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/Manifest b/sci-biology/ncbi-tools/Manifest
index 69ac91f2a963..4e2502922381 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,6 +1,3 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
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 MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
 RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b files/21ncbi-r1 232
@@ -21,6 +18,7 @@ DIST mpiBLAST-1.4.0.tgz 344877 RMD160 ec7e7ed6be2334b1c731234c65bdd8757b770031 S
 DIST mpiblast-20060625.tar.gz 165096 RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 SHA1 e0acdde2770973b752396a6ba1a99b47ea4ddcde SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097
 DIST ncbi-tools-20050605.tar.gz 14458684 RMD160 82d3c008e9b1741e8ac286d66c1ad68693663590 SHA1 7e1ddd3f049df7c906f2681453c5e5a7b12622d8 SHA256 e0108faeb84da35da82acaa925c084fbeb455c5e571cdcaae5b02c612df46209
 DIST ncbi-tools-20060507.tar.gz 15396356 RMD160 56114d25ace0338d1ef5c8c2a3cc36ce740a12e3 SHA1 64269236b09fba29d4afe0cd8a3ac6a47fee5218 SHA256 b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129
+DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 SHA1 4e7990e9fed1cc507d10a1b5285e51dc183d318a SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
 EBUILD ncbi-tools-20050605-r2.ebuild 7006 RMD160 6b4b34d6fb3e5c83f83f96cbdf501cf9caf52fd7 SHA1 f704742dfb43e554874c1b5691910072f8e944ec SHA256 2607ff37cf893e92359987972384e099e7152294c65c93cd6a6da9334aae689f
 MD5 3d7210703a9b44f5b7bb11298eb4848a ncbi-tools-20050605-r2.ebuild 7006
@@ -34,10 +32,14 @@ EBUILD ncbi-tools-20060507.ebuild 6404 RMD160 5b3da85bd685bd72d0e50726afa0814de4
 MD5 b81b36665616d2e18c075acba4c3b289 ncbi-tools-20060507.ebuild 6404
 RMD160 5b3da85bd685bd72d0e50726afa0814de4027c83 ncbi-tools-20060507.ebuild 6404
 SHA256 c583a88edcb81f312927254be5052ee353818ebdadc8faf7f062e2cc50394553 ncbi-tools-20060507.ebuild 6404
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-SHA256 9bb96be997943dfaa1ea002b1363af08ad8bc3c914535fa81b3397d9ae65dc01 ChangeLog 11131
+EBUILD ncbi-tools-20061015.ebuild 6412 RMD160 315191efc3ae1cbe17069cda2a6e759734ac800b SHA1 be9079c6baab91128edc9f0d6743f657360c8572 SHA256 d12c8cb1f1b04455c375b4e1416b55af676a35274bbe9028251150964a0bb80c
+MD5 4d1e3aa7575d583fba120b108d351504 ncbi-tools-20061015.ebuild 6412
+RMD160 315191efc3ae1cbe17069cda2a6e759734ac800b ncbi-tools-20061015.ebuild 6412
+SHA256 d12c8cb1f1b04455c375b4e1416b55af676a35274bbe9028251150964a0bb80c ncbi-tools-20061015.ebuild 6412
+MISC ChangeLog 11279 RMD160 8b3db57249684b6eec998a9a80e5f69ec237a7ef SHA1 112ed20b5866a684fd224fa43dc2328ddcde739d SHA256 f42af77a37cf9d478737a97f4a539e348e711a0cee8d6c615f3f11d548f4dbeb
+MD5 9f1d3ff16f6c7de8390949d0a73b35c5 ChangeLog 11279
+RMD160 8b3db57249684b6eec998a9a80e5f69ec237a7ef ChangeLog 11279
+SHA256 f42af77a37cf9d478737a97f4a539e348e711a0cee8d6c615f3f11d548f4dbeb ChangeLog 11279
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
 MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
@@ -51,10 +53,6 @@ SHA256 3accc0c62ee18b7ad56d3d6005fb33add90a80503e22c53792cf7a9686b92c21 files/di
 MD5 96f59d6f4dcd072b2744878ce377b23d files/digest-ncbi-tools-20060507 777
 RMD160 d0a656e48f738e1a30061121a7fecf6e5b7ee841 files/digest-ncbi-tools-20060507 777
 SHA256 d20530e140a48cab2fc12df5a0bf0957e956a6ea35a07b5b5ed42a43466ad4d7 files/digest-ncbi-tools-20060507 777
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-RjQiPxicMAUvtA6SkVRpgeM=
-=DcHK
------END PGP SIGNATURE-----
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+RMD160 82eefb533a71585a5526c9762f9b389341863252 files/digest-ncbi-tools-20061015 777
+SHA256 8dcb338c684c40627c2cfd3a425654b91b29f76804b3c14dde7e4bc4857e3031 files/digest-ncbi-tools-20061015 777
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 @@
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+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."
+}