Version bump, take maintainership

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

4 files changed, 194 insertions, 3 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 8e90b0ae5272..cb64a9fa50b6 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 1.69 2009/04/19 21:10:42 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.70 2009/09/04 18:12:02 weaver Exp $
+
+*ncbi-tools-20090809 (04 Sep 2009)
+
+  04 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> metadata.xml,
+  +ncbi-tools-20090809.ebuild:
+  Version bump, take maintainership
 
   19 Apr 2009; Brent Baude <ranger@gentoo.org> ncbi-tools-20090301.ebuild:
   Marking ncbi-tools-20090301 ~ppc64 for bug 266569
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 6fa33b746fff..a7e39558c68c 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -8,6 +8,7 @@ DIST ncbi-tools-20060507.tar.gz 15396356 RMD160 56114d25ace0338d1ef5c8c2a3cc36ce
 DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 SHA1 4e7990e9fed1cc507d10a1b5285e51dc183d318a SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de
 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-20090809.tar.gz 64646971 RMD160 a1482a252647b2ea878ac9b08093cfd48bfaa82a SHA1 9727c13d94cc06cfe2f70148fa6bc5dfe011af50 SHA256 0c874961baf1bbfde9c209cc65fdcc5fe07f6f644b69674a89703b6726b66b15
 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
@@ -15,5 +16,6 @@ EBUILD ncbi-tools-20061015-r1.ebuild 6516 RMD160 71ce04a50d4112108796258757fb10d
 EBUILD ncbi-tools-20070826.ebuild 7143 RMD160 4c276b590925dfd3d31e354a2942db4e502adcd9 SHA1 f6a50ad5f18b56490f542fd8ba641142df202b4f SHA256 34d6b65d94e7ce07a21aa691618dbabaa0e20655b86ab01f98f1681ed3e675aa
 EBUILD ncbi-tools-20080302.ebuild 7142 RMD160 e3075bab7683b75cf57d6d05649d439a4c97889a SHA1 cbf189eb91175135b765d532eed3569a1b254900 SHA256 c68218365e73bb1cc38bf7e7003d52789e39bd23e5a77a6ed94a75441cff5b33
 EBUILD ncbi-tools-20090301.ebuild 6146 RMD160 941ffe271ff17e5506d22546503bcb58365395c7 SHA1 052310bc4c523e475c33cd0aa1445e59bac0987a SHA256 61eabbff00d4d47c9884fef0e59225edf21ec0ae471c5244bb0b7d9659f6adc7
-MISC ChangeLog 14518 RMD160 20801608c30edbf3039c1ee545d8f711c9561d22 SHA1 2e908ce29000d8786d402d28d6564573db522843 SHA256 43f1c73a92737890ddd453d99183fcab34540597ff239f333c05f0126c0aae9f
-MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+EBUILD ncbi-tools-20090809.ebuild 6107 RMD160 3a8347f107d568b770e3abee6868a93c04bc4dd4 SHA1 317c6ef33c25bbb98d437d52388b17d5b986b82e SHA256 3b4ad929ced4c5bea0bfac064a386b6779d3694eb2ad9e480eb7c281becbf854
+MISC ChangeLog 14686 RMD160 e5bf0089c2c60628219fd295e0c4eeac0b9b31a1 SHA1 180f54c796f9891470cbd5eb464d0398eb01f23d SHA256 6a663e353d8537b57a47c91b149c619892c824fa92c7792d5cad1f4ebde8480a
+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
index d4648212cbad..3302123e5718 100644
--- a/sci-biology/ncbi-tools/metadata.xml
+++ b/sci-biology/ncbi-tools/metadata.xml
@@ -1,5 +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-20090809.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
new file mode 100644
index 000000000000..9b52e0c80545
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
@@ -0,0 +1,179 @@
+# 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-20090809.ebuild,v 1.1 2009/09/04 18:12:02 weaver Exp $
+
+EAPI="2"
+
+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="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~x86"
+
+# IUSE=mpi deprecated, use sci-biology/mpiblast separately
+IUSE="doc X"
+
+RDEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	X? ( x11-libs/openmotif )"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/ncbi"
+
+EXTRA_VIB="asn2all asn2asn"
+
+pkg_setup() {
+	echo
+	ewarn 'Please note that the NCBI toolkit (and especially the X'
+	ewarn 'applications) are known to have compilation and run-time'
+	ewarn 'problems when compiled with agressive compilation flags. The'
+	ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
+	ewarn 'X support is enabled.'
+	echo
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-extra_vib.patch
+
+	if use ppc || use ppc64; then
+		epatch "${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."
+}