[gentoo-commits] gentoo-x86 commit in sci-biology/ncbi-tools: ChangeLog ncbi-tools-2.2.26-r2.ebuild ncbi-tools-2.2.26-r1.ebuild

[Justin Lecher (jlec)]

jlec        13/03/01 14:52:32

  Modified:             ChangeLog
  Added:                ncbi-tools-2.2.26-r2.ebuild
  Removed:              ncbi-tools-2.2.26-r1.ebuild
  Log:
  sci-biology/ncbi-tools: Fix all config files, #459720, #459726, #459878
  
  (Portage version: 2.2.0_alpha163/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

Revision  Changes    Path
1.89                 sci-biology/ncbi-tools/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.89&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.89&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?r1=1.88&r2=1.89

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v
retrieving revision 1.88
retrieving revision 1.89
diff -u -r1.88 -r1.89
--- ChangeLog	1 Mar 2013 09:14:24 -0000	1.88
+++ ChangeLog	1 Mar 2013 14:52:31 -0000	1.89
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.88 2013/03/01 09:14:24 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.89 2013/03/01 14:52:31 jlec Exp $
+
+*ncbi-tools-2.2.26-r2 (01 Mar 2013)
+
+  01 Mar 2013; Justin Lecher <jlec@g.o> -ncbi-tools-2.2.26-r1.ebuild,
+  +ncbi-tools-2.2.26-r2.ebuild:
+  Fix all config files, #459720, #459726, #459878
 
 *ncbi-tools-2.2.26-r1 (01 Mar 2013)
 



1.1                  sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26-r2.ebuild?rev=1.1&content-type=text/plain

Index: ncbi-tools-2.2.26-r2.ebuild
===================================================================
# 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-r2.ebuild,v 1.1 2013/03/01 14:52:31 jlec Exp $

EAPI=5

inherit eutils flag-o-matic toolchain-funcs

DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"

SLOT="0"
LICENSE="public-domain"
KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE="doc static-libs X"

RDEPEND="
	app-shells/tcsh
	dev-lang/perl
	media-libs/libpng
	X? ( x11-libs/motif: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
		sed \
			-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
			-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
			-i "${S}"/make/makedis.csh || die
	else
		# X applications segfault on startup on x86 with -O3.
		use x86 || replace-flags '-O3' '-O2'
	fi

	# Apply user C flags...
	cd "${S}"/platform
	sed \
		-e "s:-O[s0-9]\?:asd:g" \
		-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
		-e 's:-x[A-Z]*::g' \
		-e 's:-pipe::g' \
		-e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
		-e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
		-e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
		-e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
		-e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
		-e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
		-e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
		-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
		-i * || die

	# 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 "${WORKDIR}"
	csh ncbi/make/makedis.csh || die
	mkdir "${S}"/cgi "${S}"/real || die
	mv "${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
	cp spidey ../bin/ || die
}

src_install() {
	#sci-geosciences/cdat-lite
	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die

	dobin "${S}"/bin/*

	for i in ${EXTRA_VIB}; do
		dobin "${S}"/build/${i} || die "Failed to install binaries."
	done
	use static-libs && dolib.a "${S}"/lib/*.a
	mkdir -p "${ED}"/usr/include/ncbi
	cp -RL "${S}"/include/* "${ED}"/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 "${S}"/{README,VERSION,doc/{*.txt,README.*}}
	newdoc "${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
	mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
	doman "${S}"/doc/man/*

	# Hypertext user documentation
	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
	insinto /usr/share/doc/${PF}/html
	doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install

	# Developer documentation
	if use doc; then
		# Demo programs
		mkdir "${ED}"/usr/share/ncbi
		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
	fi

	# Shared data (similarity matrices and such) and database directory.
	insinto /usr/share/ncbi
	doins -r "${S}"/data
	dodir /usr/share/ncbi/formatdb

	# Default config file to set the path for shared data.
	insinto /etc/ncbi
	newins "${FILESDIR}"/ncbirc .ncbirc

	# Env file to set the location of the config file and BLAST databases.
	newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
}