New ncbi version and cleanup of stable ebuild.

(Portage version: 2.1.3.12)

4 files changed, 263 insertions, 39 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index ed0294c7da36..4a208345ac66 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.53 2007/06/05 11:00:49 armin76 Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.54 2007/10/13 23:09:17 je_fro Exp $
+
+  13 Oct 2007; <jeff@gentoo.org> ncbi-tools-20050605.ebuild,
+  +ncbi-tools-20070826.ebuild:
+  Added quotes to make repoman happy.
+
+*ncbi-tools-20070826 (13 Oct 2007)
+
+  13 Oct 2007; <jeff@gentoo.org> +ncbi-tools-20070826.ebuild:
+  New version - mpiblast compilation broken at present.
 
   05 Jun 2007; Raúl Porcel <armin76@gentoo.org> ncbi-tools-20060507.ebuild:
   alpha stable wrt #152292
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
new file mode 100644
index 000000000000..591fbdb57d3b
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20070826
@@ -0,0 +1,9 @@
+MD5 104239a2c508de944bc68a510b4ca517 mpiblast-20070826.tar.gz 286805
+RMD160 7c79be86368cf67509c6df124f0ca10deba07d88 mpiblast-20070826.tar.gz 286805
+SHA256 0093e55fd21f16f12a39193fe26c685f9fcbd3110c8733f1de0abb8f2a6726f7 mpiblast-20070826.tar.gz 286805
+MD5 c17f7b08c12823e4320661894110dcb1 ncbi-tools-20070826.tar.gz 17076175
+RMD160 00daadd503bf729c15ada0008e305492a076fe15 ncbi-tools-20070826.tar.gz 17076175
+SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8 ncbi-tools-20070826.tar.gz 17076175
+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-20050605.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
index be09c595109a..743d24322663 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.13 2006/10/25 19:46:02 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050605.ebuild,v 1.14 2007/10/13 23:09:17 je_fro Exp $
 
 inherit flag-o-matic toolchain-funcs eutils
 
@@ -36,10 +36,10 @@ pkg_setup() {
 src_unpack() {
 	unpack ${A}
 
-	use ppc64 && cd ${S} && epatch ${FILESDIR}/${PN}-lop.patch
+	use ppc64 && cd "${S}" && epatch "${FILESDIR}/${PN}-lop.patch"
 
 	if ! use X; then
-		cd ${S}/make
+		cd "${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
@@ -51,7 +51,7 @@ src_unpack() {
 	fi
 
 	# Apply user C flags...
-	cd ${S}/platform
+	cd "${S}/platform"
 	# ... on x86...
 	sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \
 		-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \
@@ -95,19 +95,19 @@ src_unpack() {
 }
 
 src_compile() {
-	cd ${WORKDIR}
+	cd "${WORKDIR}"
 	ncbi/make/makedis.csh || die
-	mkdir ${S}/cgi
-	mkdir ${S}/real
-	mv ${S}/bin/*.cgi ${S}/cgi
-	mv ${S}/bin/*.REAL ${S}/real
+	mkdir "${S}/cgi"
+	mkdir "${S}/real"
+	mv "${S}/bin/*.cgi" "${S}/cgi"
+	mv "${S}/bin/*.REAL" "${S}/real"
 }
 
 src_install() {
-	dobin ${S}/bin/*
-	dolib ${S}/lib/*
-	mkdir -p ${D}/usr/include/ncbi
-	cp -RL ${S}/include/* ${D}/usr/include/ncbi
+	dobin "${S}/bin/*"
+	dolib "${S}/lib/*"
+	mkdir -p "${D}/usr/include/ncbi"
+	cp -RL "${S}/include/*" "${D}/usr/include/ncbi"
 
 	# TODO: Web apps
 	#insinto /usr/share/ncbi/lib/cgi
@@ -117,53 +117,53 @@ src_install() {
 	# TODO: Add support for wwwblast.
 
 	# Basic documentation
-	dodoc ${S}/{README,VERSION,doc/{*.txt,README.asn2xml}}
-	newdoc ${S}/doc/fa2htgs/README README.fa2htgs
-	newdoc ${S}/config/README README.config
-	newdoc ${S}/network/encrypt/README README.encrypt
-	newdoc ${S}/network/nsclilib/readme README.nsclilib
-	newdoc ${S}/sequin/README README.sequin
-	doman ${S}/doc/man/*
+	dodoc "${S}/{README,VERSION,doc/{*.txt,README.asn2xml}}"
+	newdoc "${S}/doc/fa2htgs/README README.fa2htgs"
+	newdoc "${S}/config/README README.config"
+	newdoc "${S}/network/encrypt/README README.encrypt"
+	newdoc "${S}/network/nsclilib/readme README.nsclilib"
+	newdoc "${S}/sequin/README README.sequin"
+	doman "${S}/doc/man/*"
 
 	# Hypertext user documentation
-	dohtml ${S}/{README.html,doc/{*.html *.gif}}
+	dohtml "${S}/{README.html,doc/{*.html *.gif}}"
 	insinto /usr/share/doc/${PF}/html/blast
-	doins ${S}/doc/blast/*
+	doins "${S}/doc/blast/*"
 
 	# Developer documentation
 	if use doc; then
 		# "socks" documentation
 		SOCKS="network/socks/socks.cstc.4.2"
 		insinto /usr/share/doc/${PF}/socks
-		doins ${S}/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects}
-		newins ${S}/${SOCKS}/libident/README README.libident
-		doins ${S}/${SOCKS}/sockd/sockd.conf.sample
-		doman ${S}/${SOCKS}/{doc/*.{1,5,8},libident/ident.3}
+		doins "${S}/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects}"
+		newins "${S}/${SOCKS}/libident/README README.libident"
+		doins "${S}/${SOCKS}/sockd/sockd.conf.sample"
+		doman "${S}/${SOCKS}/{doc/*.{1,5,8},libident/ident.3}"
 		# "regexp" documentation
 		insinto /usr/share/doc/${PF}/regexp
-		doins ${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}
+		doins "${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt}"
 		insinto /usr/share/doc/${PF}/regexp/html
-		doins ${S}/regexp/doc/*.html
-		doman ${S}/regexp/doc/*.{1,3}
+		doins "${S}/regexp/doc/*.html"
+		doman "${S}/regexp/doc/*.{1,3}"
 		# Hypertext SDK documentation
 		insinto /usr/share/doc/${PF}/html/sdk
-		doins ${WORKDIR}/${PN}-sdk-doc/*
+		doins "${WORKDIR}/${PN}-sdk-doc/*"
 		# Demo programs
-		mkdir ${D}/usr/share/ncbi
-		mv ${S}/demo ${D}/usr/share/ncbi/demo
-		mv ${S}/regexp/demo ${D}/usr/share/ncbi/demo/regexp
-		mv ${S}/regexp/test ${D}/usr/share/ncbi/demo/regexp/test
+		mkdir "${D}/usr/share/ncbi"
+		mv "${S}/demo ${D}/usr/share/ncbi/demo"
+		mv "${S}/regexp/demo" "${D}/usr/share/ncbi/demo/regexp"
+		mv "${S}/regexp/test" "${D}/usr/share/ncbi/demo/regexp/test"
 	fi
 
 	# Shared data (similarity matrices and such) and database directory.
 	insinto /usr/share/ncbi/data
-	doins ${S}/data/*
+	doins "${S}/data/*"
 	dodir /usr/share/ncbi/formatdb
 
 	# Default config file to set the path for shared data.
 	insinto /etc/ncbi
-	newins ${FILESDIR}/ncbirc .ncbirc
+	newins "${FILESDIR}/ncbirc" .ncbirc
 
 	# Env file to set the location of the config file and BLAST databases.
-	newenvd ${FILESDIR}/21ncbi-r1 21ncbi
+	newenvd "${FILESDIR}/21ncbi-r1" 21ncbi
 }
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
new file mode 100644
index 000000000000..2707d0ce1835
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
@@ -0,0 +1,206 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild,v 1.1 2007/10/13 23:09:17 je_fro 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-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"
+
+DEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	sys-devel/pmake
+	mpi? ( virtual/mpi )
+	X? ( virtual/motif )"
+
+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 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() {
+	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="${WORKDIR}"/ncbi --with-mpi=/usr || die
+#		emake || die
+#	fi
+}
+
+src_install() {
+	dobin "${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."
+}