Version bump

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

3 files changed, 195 insertions, 2 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index ecfc0c194c87..1eb706f2f465 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.66 2009/03/24 21:07:55 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.67 2009/04/17 18:25:28 weaver Exp $
+
+*ncbi-tools-20090301 (17 Apr 2009)
+
+  17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org>
+  +ncbi-tools-20090301.ebuild:
+  Version bump, minor cleanup
 
   24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
   Giving up maintainership of this package.
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 3f7256bd92b6..8a11d5fc9e51 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -9,9 +9,11 @@ DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270
 DIST ncbi-tools-20070826.tar.gz 17076175 RMD160 00daadd503bf729c15ada0008e305492a076fe15 SHA1 5e61f4f73ef52d145d0df86bb00f03f2db833ee9 SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8
 DIST ncbi-tools-20080302.tar.gz 17294669 RMD160 e269bcadc9e498163252e348a314bab8d0ece8f6 SHA1 d91a66bafac62dd07cc2e524874492388e5a780d SHA256 93a30ec0a6e408858c6364039a4eb240d9fadaf8ce670a14151e03c5169a12c1
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
+DIST ncbi.tar.gz 64548732 RMD160 fc15c1e6ab68a6b45fb70f17e88905fee68240c0 SHA1 89cfde43423ffcec9588fa9295a875ee22967c63 SHA256 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
 EBUILD ncbi-tools-20060507.ebuild 6428 RMD160 244feb61ad1dbb37090e5940526f0fc5a67390bf SHA1 298d7e6a207ee394438cb998a2886c8fc7077eeb SHA256 c9ef92fb8c4b8ac18d2fd654b57e2e090f1a6feffe33c5ee0049e617ec838215
 EBUILD ncbi-tools-20061015-r1.ebuild 6516 RMD160 71ce04a50d4112108796258757fb10d82b481ef9 SHA1 ac688ece6074201fc535e1a5c2d396311079b55a SHA256 77ad207082d5ec9ba5a9ef562e0639b9ef9d4382ba969f889143ed120425500d
 EBUILD ncbi-tools-20070826.ebuild 7143 RMD160 4c276b590925dfd3d31e354a2942db4e502adcd9 SHA1 f6a50ad5f18b56490f542fd8ba641142df202b4f SHA256 34d6b65d94e7ce07a21aa691618dbabaa0e20655b86ab01f98f1681ed3e675aa
 EBUILD ncbi-tools-20080302.ebuild 7142 RMD160 e3075bab7683b75cf57d6d05649d439a4c97889a SHA1 cbf189eb91175135b765d532eed3569a1b254900 SHA256 c68218365e73bb1cc38bf7e7003d52789e39bd23e5a77a6ed94a75441cff5b33
-MISC ChangeLog 14125 RMD160 1aa9924b046406b402bee2ab145467ac5b600069 SHA1 69343899cdccc8e65e394a472e487b65cfdac860 SHA256 945679c9e9a1e3f78cd5a10711c8835cbdf88a254dcf4ccad913b6caeeba87f2
+EBUILD ncbi-tools-20090301.ebuild 6132 RMD160 a8043d4b024a4abecd6d046af2ddf062adfe6d9d SHA1 18f0ee83a533973bf9c23141855114e692fec1d4 SHA256 dca0a8c717286bb682238dee86b4ce662774a44e91220be5828592c3dd800812
+MISC ChangeLog 14271 RMD160 37338b423f0b6f5f913c2aaffd06425fc4a76cae SHA1 b35832bbb6ea1571343f6766aa13647bd137fa68 SHA256 48cb9a201fa31fde0cb183552399246d06e37f60a3c73d424c5cad2ead682885
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild
new file mode 100644
index 000000000000..33e57a26fd69
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild
@@ -0,0 +1,185 @@
+# 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-20090301.ebuild,v 1.1 2009/04/17 18:25:28 weaver Exp $
+
+EAPI="1"
+
+inherit flag-o-matic toolchain-funcs eutils
+
+DESCRIPTION="Development toolkit and applications for computational biology"
+LICENSE="public-domain"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+
+#SRC_URI="mirror://gentoo/${P}.tar.gz"
+SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# IUSE=mpi deprecated, use sci-biology/mpiblast separately
+IUSE="doc X"
+
+RDEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	X? ( x11-libs/openmotif )"
+
+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_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	epatch "${FILESDIR}"/${PN}-extra_vib.patch
+
+	if use ppc64; then
+		epatch "${FILESDIR}"/${PN}-lop.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 64-bit 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 linux64.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 64-bit Linux...
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
+	# ... on generic Linux.
+	sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
+
+	# We use dynamic libraries
+	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
+}
+
+src_compile() {
+	export EXTRA_VIB
+	cd "${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
+}
+
+src_install() {
+	dobin "${S}"/bin/* || die "Failed to install binaries."
+	for i in ${EXTRA_VIB}; do
+		dobin "${S}"/build/${i} || die "Failed to install binaries."
+	done
+	dolib "${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."
+
+	# 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.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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
+
+	# Developer documentation
+	if use doc; then
+		# Demo programs
+		mkdir "${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."
+}