sci-biology/ncbi-tools: Drop old; rename fmerge.1 to fmerg-ncbi.1 -> resolves collision with dev-util/fhist, #429560

Package-Manager: portage-2.2.0_alpha163/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

8 files changed, 35 insertions, 438 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 26cc14f56f53..b74895569524 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.86 2012/10/24 19:31:33 ulm Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.87 2013/02/18 12:53:27 jlec Exp $
+
+  18 Feb 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-0.20080302.ebuild,
+  ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild,
+  -ncbi-tools-20080302.ebuild, -ncbi-tools-20090809.ebuild, metadata.xml:
+  Drop old; rename fmerge.1 to fmerg-ncbi.1 -> resolves collision with
+  dev-util/fhist, #429560
 
   24 Oct 2012; Ulrich Müller <ulm@gentoo.org> ncbi-tools-0.20080302.ebuild,
   ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild,
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 1b5edd43dd1c..a5abd76c4d2e 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -7,31 +7,18 @@ AUX ncbi-tools-extra_vib.patch 1393 SHA256 b7639937d59c8bd636c6b02a65a4469d18864
 AUX ncbi-tools-lop.patch 701 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc SHA512 706dfb29f9b1eff1fcc7dc1df1d533563d9d12ead5b930930121ad92a3e8c159d1d7cf30acd9f4462772e8f27e6dcf45cd6125f2fa077b3902145f6faf1c8352 WHIRLPOOL 7d0a9ba13c6ede034ac71870f802ee75945e13944742ffd19086ce71127b97807ea1c87f97d6b3d7a96f5e7fb24b6110f03836a3f0967d1f23e68ca1de4e755a
 AUX ncbirc 33 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e SHA512 a3899a45ba6434ffc3dd4ea4e43979faa20f5de922fcde2c5635c8fb31c45a00d3802c300151009bb705687b2ea0ee048d62067c21d49f81cb04587ce2aa84e6 WHIRLPOOL 41ef3fd7e4bb359c5e530f7d3f4dde400ec7b479f1e28fcc2c15eef8611133d1560e9249d64d891d38bcab864c1fa2b37db67fb73a2ff1bb293ce05a49483dbd
 DIST ncbi-tools-0.20090809.tar.gz 64646971 SHA256 0c874961baf1bbfde9c209cc65fdcc5fe07f6f644b69674a89703b6726b66b15
-DIST ncbi-tools-2.2.26.tar.gz 68691452 SHA256 d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d
+DIST ncbi-tools-2.2.26.tar.gz 68691452 SHA256 d8fffac25efc8ca894c707c840a4797a8a949ae6fd983d2f91c9972f788efb7d SHA512 da167216b56386b8c91a660e8ea0f3ac39b991d4519af9e02fc26aa16ed602eb3d9d874446f69a8f6840ae31a4d5a29da170e04e8a72b56f8c3ca038d1437014 WHIRLPOOL 6f390a4487b7ebf9d5ca31018f3b33602a695e4b0a4b090952fec9c7e8c3956edc197e75ffd32588f9431cc04b4262a2ca2e3b0ba50dd622ed73a4da6655a956
 DIST ncbi-tools-20080302.tar.gz 17294669 SHA256 93a30ec0a6e408858c6364039a4eb240d9fadaf8ce670a14151e03c5169a12c1
-DIST ncbi-tools-20090809.tar.gz 64646971 SHA256 0c874961baf1bbfde9c209cc65fdcc5fe07f6f644b69674a89703b6726b66b15
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
-EBUILD ncbi-tools-0.20080302.ebuild 7152 SHA256 ca087f0425f6473f622e7418e8a55b7101e4c4c27e4165383168787e74cdc1cd SHA512 f73e0b6ce7a8440ca76229b374573698faa464bea24cae9693ccaca296082d530cdaae190d289418eb885ebbdb70df7df2b7ca895c08d9aca3041b1a5d7bc925 WHIRLPOOL 86210eb90d23998689d2c059cca9dd5369ae535739963f178a94c497fb799daae20441d454302a5fae28591b67ca4bbc5f998aae2c8ed51703d8437a9c2f9ea5
-EBUILD ncbi-tools-0.20090809.ebuild 6134 SHA256 f02351b7dfe314f3ef8a11ef1f6091b93455f76f6478aa414fb52d4a524af4f9 SHA512 24be98cefc7349f970647111c2ee5862f784f352a195dfeac69cb83c7602ef8ee543f8ddd45990d92776c60eebabac96f2804fb95e73d75bc40aca976a4c7500 WHIRLPOOL 67d0ca3bef14abd504993c7c0bfdcd490abbe483485e0b1a9300ec3f8c01527f8e3d71e0283460ce7078075b86e991e45a3b4175e5dcc097dbb55a3538a59acb
-EBUILD ncbi-tools-2.2.26.ebuild 4527 SHA256 6b7ceb2b256712f2de51c13b047e1c775196f642036601e369dead76f4a5ac33 SHA512 44a839da36b22c68dde2f58c71b4f01a13ca3f0b95954284ce3a90d86291e0ada479fd30a3e429af00c139cf35af7cc648301e162ea973bd6ee0048d5b4e580d WHIRLPOOL 27fafa31ada8e4e8d759816e76b26fbea677fcde9c7e116d3a43aec1a99419e27a186a617ca3521599579b283a918af0e45cb9b2fbab39bdffbbe5ec8ed524f8
-EBUILD ncbi-tools-20080302.ebuild 7137 SHA256 6acb768814e57b8f3a62e0278f7a99f5f09f80b99b243e8894813cb89c1c4319 SHA512 a63f7cf5a362e1a59f5c5f73125a02433a989f7d7700055b3b1c9c56145c3c0586193941a686982fc029fa9a53bff4c781ec2bf03326164246644013aa8f8292 WHIRLPOOL 1422c45de9150a8a7ab6281f212599244ff61fb909c6fc392ea0b55ad22df739ccee33dd99a0f8e2c247e218206d00996fee4219dce0e365d7ce9aa41353feb8
-EBUILD ncbi-tools-20090809.ebuild 6128 SHA256 e9673ce3861699343452451c06cbc85e0ddd50af9353e9747ec7452ad53cde3e SHA512 6712b56399d1b71ac2e37d1e5ae67d6d0f250b7d501581cdc91143ed8848103b534d85c69951443fd35b16355543bc7384d6230a2f2ce38bce146bd862e13a00 WHIRLPOOL 4ce2de2c552f5d82f9fab83ca78b7f590ec129682db18396e26719e789cda2ed82a05740517a4f2ab620223b98a696367f72d077e89a26fff1182b2cad6b3b83
-MISC ChangeLog 17431 SHA256 49d00bf0046770789729ffef23d55a0147b6d8208cfbd0d74d879c8b4dcabb13 SHA512 6e94e9b653220a11c5bc18e08f440632b09773bbf7b2bd7a2b50b817f8340f2d0a9553034e75022152a6ecca15edf6c051a64c575e793f92131a1c6c6cd6453d WHIRLPOOL 0ec74d93e5e55a085d91165b71cf82f30f3202ec2f0de5f4bc67caf0cb46ccda2f9d5de66328da4ab152f31d501e834af3984e1ad1280038d5fc67de18627dbd
-MISC metadata.xml 259 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 SHA512 c3aea4d69d75075af0108a03b7e109cfed6a1fe324f8ccbda3d4e5ca8a5070f1b24ddeb46b64787e10fd22252d867abcee1f31316d602f7e32fe3c990ae60d74 WHIRLPOOL e50da2f26fd4c908446d22da3edb595d60e61d72def374be46440358802a211fc34045b7ad970c4f94b57f7b17ff24cfe64dc94254fea20e047f1fbbbcae0c64
+EBUILD ncbi-tools-0.20080302.ebuild 7172 SHA256 0cb4afa52072d210070446bbf5087488c8ec5d9606552cc12fb600429461acff SHA512 c01be3c1468862020b9d43bc3e14bd5a165058e33cb507ae7ddaafa7c0df5ea06df04306dea4c082b00b2a3aa910a8b60db82185de2e57ae37b5d08a3a34dca7 WHIRLPOOL 7a5d5f83c033b45a9456af36c80a2a8c9be3eff253709aabb2251209463bf1b5999b650d9aeba4563715691ae8052fbe8afaeb513f7303e3e60c84747ddd5949
+EBUILD ncbi-tools-0.20090809.ebuild 6154 SHA256 5ca2bff0d8ec0883db98f2b855e1a58adb63bda490a0572c52adbe8455837444 SHA512 b5f10ce32bdce79c8b4d6faecc5d1c7b9930011a4f0f0c8f5bb7453e874e9b461176cbb684e04b925a95e0bbc615c8c349eac72a25c85ac42b16810b0fe91af4 WHIRLPOOL 07487e7f2fe84c5850c4af595a744fd55335c736be08f6651053c2ec9eef2e4968e50a12ff98d0da18b7ab8464f5a3d1cee260d9626843fbdc40dc8e34a9960c
+EBUILD ncbi-tools-2.2.26.ebuild 4571 SHA256 8a345ab1cbf762aebb79fbe3fd07b5026060184db8ad364c62442b4f341f6abe SHA512 58f838b40ed9f24c12ec6a744055b538bb84e55315ba5b2f9c8e56b9f507f307f00ed0b8e6dd3cf18020c0e8ce9aaa51a84bd02874ba4ae7df88a86830c0986f WHIRLPOOL 121f00ef6075162a84b5eb1dc571443d26a81ff2dc27d4500ad970a640a40e1deeba6b95259a5a738fad2e5e68654ab352a59a118958ea4c58755d8ab1376dc9
+MISC ChangeLog 17739 SHA256 ba1a3579721c05a7c6c2e5ee6ec90f4fbb66282171dd3f3457a68bfbb68dd1ab SHA512 a764bd6228591b6f38f08fc2828cb99857a1672285a5c67525e15799270f3506333a104d58272b6277ce9be20df5809e80203d5c6e40ef3e78167fdde99669be WHIRLPOOL df3cfc996c1678c5a965588bd79cb4bb7469854236203927366d702295c194d19d2df7e17fa7de0a99e06b4c21d57174a8f450f5c9ccada3ab7b781d967a3a34
+MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
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diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/ncbi-tools/metadata.xml
+++ b/sci-biology/ncbi-tools/metadata.xml
@@ -1,9 +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>
+  <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-0.20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
index ed292e2f2873..6d354f01c39f 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild,v 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
 
 EAPI=1
 
@@ -24,8 +24,10 @@ KEYWORDS="~alpha amd64 ~ppc ppc64 ~sparc x86"
 
 IUSE="doc X"
 
-RDEPEND="app-shells/tcsh
+RDEPEND="
+	app-shells/tcsh
 	dev-lang/perl
+	!dev-util/fhist
 	media-libs/libpng
 	X? ( >=x11-libs/motif-2.3:0 )"
 
diff --git a/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
index 2d3c2dfd5c12..16c94b205bde 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild,v 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
 
 EAPI="2"
 
@@ -17,8 +17,10 @@ KEYWORDS="~alpha amd64 ~ppc64 x86"
 # IUSE=mpi deprecated, use sci-biology/mpiblast separately
 IUSE="doc X"
 
-RDEPEND="app-shells/tcsh
+RDEPEND="
+	app-shells/tcsh
 	dev-lang/perl
+	!dev-util/fhist
 	media-libs/libpng
 	X? ( >=x11-libs/motif-2.3:0 )"
 DEPEND="${RDEPEND}"
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
index 14fbd62bec8e..bc6bc16b9064 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 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 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
 
 EAPI=4
 
@@ -121,6 +121,7 @@ src_install() {
 	newdoc "${S}"/network/encrypt/README README.encrypt
 	newdoc "${S}"/network/nsclilib/readme README.nsclilib
 	newdoc "${S}"/sequin/README README.sequin
+	mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
 	doman "${S}"/doc/man/*
 
 	# Hypertext user documentation
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
deleted file mode 100644
index a00a280cac3b..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
+++ /dev/null
@@ -1,222 +0,0 @@
-# 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-20080302.ebuild,v 1.9 2012/10/24 19:31:33 ulm 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/${P}.tar.gz
-	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )"
-
-#	mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc ppc64 ~sparc x86"
-
-# IUSE="doc mpi X"
-# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release.
-# Currently seeking a fix.
-
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( >=x11-libs/motif-2.3:0 )"
-
-DEPEND="${RDEPEND}
-		sys-devel/pmake"
-
-#	mpi? ( virtual/mpi )
-
-S="${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 mpi; then
-#		cd "${WORKDIR}"
-#		epatch "${WORKDIR}"/mpiblast/ncbi_Mar2007_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 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 = $(tc-getCC)/" linux.ncbi.mk || die
-
-	# We use dynamic libraries
-	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	# GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
-	# instead. The right solution would be to fix the Makefiles. (Be my guest.)
-	cd "${S}"/make
-	sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \
-			"Failed to replace make by pmake."
-}
-
-src_compile() {
-	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 "${S}"/real || die
-
-# mpiblast fails to compile... perhaps mpiblast2 contain a fix
-#	if use mpi; then
-#		cd "${WORKDIR}"/mpiblast
-#		AM_OPT="-a"
-#		eautoreconf
-#		econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr
-#		emake || die
-#	fi
-}
-
-src_install() {
-	dobin "${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/* "${D}"/usr/include/ncbi || \
-		die "Failed to install headers."
-
-#	if use mpi; then
-#		cd "${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."
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
deleted file mode 100644
index a744b4572c04..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
+++ /dev/null
@@ -1,179 +0,0 @@
-# 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-20090809.ebuild,v 1.6 2012/10/24 19:31:33 ulm Exp $
-
-EAPI="2"
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
-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 -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 x86"
-
-# IUSE=mpi deprecated, use sci-biology/mpiblast separately
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
-	dev-lang/perl
-	media-libs/libpng
-	X? ( >=x11-libs/motif-2.3:0 )"
-DEPEND="${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}"/${PN}-lop.patch
-	fi
-
-	if ! use X; then
-		cd "${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."
-}