New upstream version. Switched from GNU make to pmake (fixes bug #136904). Compile and install asn2all (fixes bug #136206). ppc64 keyword dropped as pmake is not available for that arch.

(Portage version: 2.1-r1)

6 files changed, 249 insertions, 2 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index f3446d09456c..861dddd08051 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.38 2006/02/01 09:10:15 spyderous Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.39 2006/06/26 17:24:32 ribosome Exp $
+
+*ncbi-tools-20060507 (26 Jun 2006)
+
+  26 Jun 2006; Olivier Fisette <ribosome@gentoo.org>
+  +files/ncbi-tools-asn2all.patch, +ncbi-tools-20060507.ebuild:
+  New upstream version. Switched from GNU make to pmake as GNU make 3.81 is
+  confused by some Makefiles (fixes bug #136904, thanks to Greg Wilson for
+  reporting). Compile and install asn2all (fixes bug #136206, thanks to José
+  María Fernández González for the suggestion). Minor bugfixes and ebuild
+  clean-up. ppc64 keyword dropped as pmake is not available for that arch.
 
   01 Feb 2006; Donnie Berkholz <spyderous@gentoo.org>;
   ncbi-tools-20050605.ebuild, ncbi-tools-20050605-r2.ebuild:
diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605
index f3e9e71cec8d..23670d7af649 100644
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605
@@ -1,2 +1,4 @@
 MD5 61864b4999390eb69e60734b3b02c149 ncbi-tools-20050605.tar.gz 14458684
 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/files/digest-ncbi-tools-20050605-r2 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
index 416d3489a46f..228d93bd444e 100644
--- a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20050605-r2
@@ -1,3 +1,7 @@
+MD5 76a5f1b547b40dcb00ae3790579dba1b mpiBLAST-1.4.0.tgz 344877
+RMD160 ec7e7ed6be2334b1c731234c65bdd8757b770031 mpiBLAST-1.4.0.tgz 344877
+SHA256 e95a4c88642790399a888f10c240733b9cf281398f931172ff8fbc56b0706cee mpiBLAST-1.4.0.tgz 344877
 MD5 61864b4999390eb69e60734b3b02c149 ncbi-tools-20050605.tar.gz 14458684
 MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
-MD5 76a5f1b547b40dcb00ae3790579dba1b mpiBLAST-1.4.0.tgz 344877
+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/files/digest-ncbi-tools-20060507 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20060507
new file mode 100644
index 000000000000..f3931295dbf1
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20060507
@@ -0,0 +1,9 @@
+MD5 14ee6d612d0d86e0dee7eb5f0c38839f mpiblast-20060625.tar.gz 165096
+RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 mpiblast-20060625.tar.gz 165096
+SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097 mpiblast-20060625.tar.gz 165096
+MD5 1c00462385fbf382c99ff65f34c0d09a ncbi-tools-20060507.tar.gz 15396356
+RMD160 56114d25ace0338d1ef5c8c2a3cc36ce740a12e3 ncbi-tools-20060507.tar.gz 15396356
+SHA256 b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129 ncbi-tools-20060507.tar.gz 15396356
+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/files/ncbi-tools-asn2all.patch b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
new file mode 100644
index 000000000000..1cd7976af599
--- /dev/null
+++ b/sci-biology/ncbi-tools/files/ncbi-tools-asn2all.patch
@@ -0,0 +1,27 @@
+--- ncbi-20050605/make/makedis.csh	2005-05-13 05:42:12.000000000 +0200
++++ ncbi/make/makedis.csh	2005-09-20 22:02:38.000000000 +0200
+@@ -472,6 +472,24 @@
+ 
+ set net_stat = $status
+ 
++if ("$?NCBI_MT_OTHERLIBS" == "1") then
++	set CMD='make $MFLG -f makenet.unx \
++		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++		THREAD_OBJ=$NCBI_THREAD_OBJ \
++		THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \
++		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++else
++	set CMD='make $MFLG -f makenet.unx \
++		CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE\" \
++		LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \
++		AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" RAN=\"$NCBI_RANLIB\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \
++		NETENTREZVERSION=\"$NETENTREZVERSION\" $NET_VIB asn2all'
++endif
++eval echo $CMD
++eval echo $CMD | sh 
++
+ if ($make_stat != 0 || $demo_stat != 0 || $threaded_demo_stat != 0 || $net_stat != 0) then
+    echo FAILURE primary make status = $make_stat, demo = $demo_stat, threaded_demo = $threaded_demo_stat, net = $net_stat
+ 	cat <<EOF
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild
new file mode 100644
index 000000000000..410e8126a5d0
--- /dev/null
+++ b/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild
@@ -0,0 +1,195 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20060507.ebuild,v 1.1 2006/06/26 17:24:32 ribosome 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-20060625.tar.gz )"
+
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc ~ppc-macos ~sparc ~x86"
+IUSE="doc mpi X"
+
+DEPEND="app-shells/tcsh
+	dev-lang/perl
+	media-libs/libpng
+	sys-devel/pmake
+	mpi? ( virtual/mpi )
+	X? ( virtual/motif )"
+
+S="${WORKDIR}/ncbi"
+
+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}-asn2all.patch
+
+	if use ppc64; then
+		epatch "${FILESDIR}"/${P}-lop.patch
+	fi
+
+	if use mpi; then
+		cd "${WORKDIR}"
+		epatch "${WORKDIR}"/mpiblast/ncbi_Dec2005_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() {
+	cd "${WORKDIR}"
+	ncbi/make/makedis.csh || die
+	mkdir "${S}"/cgi
+	mkdir "${S}"/real
+	mv "${S}"/bin/*.cgi "${S}"/cgi || die
+	mv "${S}"/bin/*.REAL "${S}"/real || die
+
+	if use mpi; then
+		cd "${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."
+	dobin "${S}"/build/asn2all || die "Failed to install binaries."
+	dolib "${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."
+}