sci-biology/ncbi-tools: Change Version numbers from x to 0.x in order to be able to follow upstream new versioning scheme; Drop old unstable

(Portage version: 2.2.0_alpha110/cvs/Linux x86_64, RepoMan options: --force)

3 files changed, 251 insertions, 37 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index e274e46a652b..5d5fe315b1f4 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,14 @@
 # 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 1.84 2012/05/22 18:32:11 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.85 2012/06/13 10:49:23 jlec Exp $
+
+*ncbi-tools-0.20090809 (13 Jun 2012)
+*ncbi-tools-0.20080302 (13 Jun 2012)
+
+  13 Jun 2012; Justin Lecher <jlec@gentoo.org> +ncbi-tools-0.20080302.ebuild,
+  +ncbi-tools-0.20090809.ebuild, -ncbi-tools-20100808.ebuild:
+  Change Version numbers from x to 0.x in order to be able to follow upstream
+  new versioning scheme; Drop old unstable
 
 *ncbi-tools-2.2.26 (22 May 2012)
 
diff --git a/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
new file mode 100644
index 000000000000..14a02acf2bd9
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
@@ -0,0 +1,223 @@
+# 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-0.20080302.ebuild,v 1.1 2012/06/13 10:49:23 jlec Exp $
+
+EAPI=1
+
+inherit flag-o-matic toolchain-funcs eutils
+
+DESCRIPTION="Development toolkit and applications for computational biology"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
+SRC_URI="
+	mirror://gentoo/${PN}-${PV/0./}.tar.gz
+	doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )"
+
+#	mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~alpha amd64 ~ppc ppc64 ~sparc x86"
+
+# IUSE="doc mpi X"
+# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release.
+# Currently seeking a fix.
+
+IUSE="doc X"
+
+RDEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	X? ( >=x11-libs/openmotif-2.3:0 )"
+
+DEPEND="${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-20100808.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
index 7bc4cb0cd59a..00cb8f688593 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
@@ -1,18 +1,18 @@
-# Copyright 1999-2010 Gentoo Foundation
+# 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-20100808.ebuild,v 1.4 2010/11/15 21:07:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild,v 1.1 2012/06/13 10:49:23 jlec Exp $
 
-EAPI="3"
+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 -> ${P}.tar.gz"
+SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV/0./}/ncbi.tar.gz -> ${P}.tar.gz"
 
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+LICENSE="public-domain"
+KEYWORDS="~alpha amd64 ~ppc64 x86"
 
 # IUSE=mpi deprecated, use sci-biology/mpiblast separately
 IUSE="doc X"
@@ -60,32 +60,32 @@ src_prepare() {
 	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} ${LDFLAGS}/" \
+		-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} ${LDFLAGS}/" \
+		-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} ${LDFLAGS}/" \
+		-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} ${LDFLAGS}/" \
+		-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} ${LDFLAGS}/" \
+		-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} ${LDFLAGS}/" \
+		-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \
 		-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \
 		-i linux.ncbi.mk || die
 
@@ -108,39 +108,26 @@ src_prepare() {
 
 	# We use dynamic libraries
 	sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
-	sed \
-		-re "s:/usr(/bin/.*sh):\1:g" \
-		-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
-		-i $(find "${S}" -type f) || die
 }
 
 src_compile() {
 	export EXTRA_VIB
 	cd "${WORKDIR}"
-	csh ncbi/make/makedis.csh || die
+	ncbi/make/makedis.csh || die
 	mkdir "${S}"/cgi
 	mkdir "${S}"/real
 	mv "${S}"/bin/*.cgi "${S}"/cgi || die
 	mv "${S}"/bin/*.REAL "${S}"/real || die
-	cd "${S}"/demo
-	emake \
-		-f ../make/makenet.unx \
-		CC="$(tc-getCC) ${CFLAGS} -I../include  -L../lib" \
-		LDFLAGS="${LDFLAGS}" \
-		spidey || die
-	cp spidey ../bin/ || die
 }
 
 src_install() {
-	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi #sci-geosciences/cdat-lite
 	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 "${ED}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
+	mkdir -p "${D}"/usr/include/ncbi
+	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
 		die "Failed to install headers."
 
 	# TODO: wwwblast with webapps
@@ -150,7 +137,7 @@ src_install() {
 	#doins ${S}/real/*
 
 	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} || \
+	dodoc "${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."
@@ -166,20 +153,16 @@ src_install() {
 		die "Failed to install man pages."
 
 	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} || \
+	dohtml "${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."
-	insinto /usr/share/doc/${PF}/html/images
-	doins "${S}"/doc/images/* || die "Failed to install documentation images."
-	insinto /usr/share/doc/${PF}/html/seq_install
-	doins "${S}"/doc/seq_install/* || die "Failed to install seq_install documentation."
 
 	# Developer documentation
 	if use doc; then
 		# Demo programs
-		mkdir "${ED}"/usr/share/ncbi
-		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
+		mkdir "${D}"/usr/share/ncbi
+		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
 	fi
 
 	# Shared data (similarity matrices and such) and database directory.