* [gentoo-commits] gentoo-x86 commit in sci-biology/ncbi-tools: ChangeLog ncbi-tools-0.20080302.ebuild ncbi-tools-0.20090809.ebuild ncbi-tools-20100808.ebuild
@ 2012-06-13 10:49 Justin Lecher (jlec)
0 siblings, 0 replies; only message in thread
From: Justin Lecher (jlec) @ 2012-06-13 10:49 UTC (permalink / raw
To: gentoo-commits
jlec 12/06/13 10:49:23
Modified: ChangeLog
Added: ncbi-tools-0.20080302.ebuild
ncbi-tools-0.20090809.ebuild
Removed: ncbi-tools-20100808.ebuild
Log:
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)
Revision Changes Path
1.85 sci-biology/ncbi-tools/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.85&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.85&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?r1=1.84&r2=1.85
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- ChangeLog 22 May 2012 18:32:11 -0000 1.84
+++ ChangeLog 13 Jun 2012 10:49:23 -0000 1.85
@@ -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)
1.1 sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild?rev=1.1&content-type=text/plain
Index: ncbi-tools-0.20080302.ebuild
===================================================================
# 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."
}
1.1 sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild?rev=1.1&content-type=text/plain
Index: ncbi-tools-0.20090809.ebuild
===================================================================
# 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-0.20090809.ebuild,v 1.1 2012/06/13 10:49:23 jlec Exp $
EAPI="2"
inherit flag-o-matic toolchain-funcs eutils
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/toolbox/ncbi_tools/old/${PV/0./}/ncbi.tar.gz -> ${P}.tar.gz"
SLOT="0"
LICENSE="public-domain"
KEYWORDS="~alpha amd64 ~ppc64 x86"
# IUSE=mpi deprecated, use sci-biology/mpiblast separately
IUSE="doc X"
RDEPEND="app-shells/tcsh
dev-lang/perl
media-libs/libpng
X? ( >=x11-libs/openmotif-2.3:0 )"
DEPEND="${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."
}
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2012-06-13 10:49 [gentoo-commits] gentoo-x86 commit in sci-biology/ncbi-tools: ChangeLog ncbi-tools-0.20080302.ebuild ncbi-tools-0.20090809.ebuild ncbi-tools-20100808.ebuild Justin Lecher (jlec)
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