From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Sel8v-0002G0-P4 for garchives@archives.gentoo.org; Wed, 13 Jun 2012 10:49:42 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 51337E044C; Wed, 13 Jun 2012 10:49:28 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 055ABE044C for ; Wed, 13 Jun 2012 10:49:27 +0000 (UTC) Received: from flycatcher.gentoo.org (flycatcher.gentoo.org [81.93.255.6]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id CD9DC1B400F for ; Wed, 13 Jun 2012 10:49:26 +0000 (UTC) Received: by flycatcher.gentoo.org (Postfix, from userid 2264) id EBF6C2004B; Wed, 13 Jun 2012 10:49:23 +0000 (UTC) From: "Justin Lecher (jlec)" To: gentoo-commits@lists.gentoo.org Reply-To: gentoo-dev@lists.gentoo.org, jlec@gentoo.org Subject: [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 X-VCS-Repository: gentoo-x86 X-VCS-Files: ChangeLog ncbi-tools-0.20080302.ebuild ncbi-tools-0.20090809.ebuild ncbi-tools-20100808.ebuild X-VCS-Directories: sci-biology/ncbi-tools X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher Content-Type: text/plain; charset=utf8 Message-Id: <20120613104923.EBF6C2004B@flycatcher.gentoo.org> Date: Wed, 13 Jun 2012 10:49:23 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: fcc03a02-58bf-45bf-b267-6a096e618c24 X-Archives-Hash: 9a9c7b259a6ea596a0010458c140fc6a 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 t= o be able to follow upstream new versioning scheme; Drop old unstable =20 (Portage version: 2.2.0_alpha110/cvs/Linux x86_64, RepoMan options: --f= orce) Revision Changes Path 1.85 sci-biology/ncbi-tools/ChangeLog file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ChangeLog?rev=3D1.85&view=3Dmarkup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ChangeLog?rev=3D1.85&content-type=3Dtext/plain diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ChangeLog?r1=3D1.84&r2=3D1.85 Index: ChangeLog =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 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 +ncbi-tools-0.20080302.eb= uild, + +ncbi-tools-0.20090809.ebuild, -ncbi-tools-20100808.ebuild: + Change Version numbers from x to 0.x in order to be able to follow ups= tream + new versioning scheme; Drop old unstable =20 *ncbi-tools-2.2.26 (22 May 2012) =20 1.1 sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ncbi-tools-0.20080302.ebuild?rev=3D1.1&view=3Dmarkup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ncbi-tools-0.20080302.ebuild?rev=3D1.1&content-type=3Dtext/plain Index: ncbi-tools-0.20080302.ebuild =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D # 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-0.20= 080302.ebuild,v 1.1 2012/06/13 10:49:23 jlec Exp $ EAPI=3D1 inherit flag-o-matic toolchain-funcs eutils DESCRIPTION=3D"Development toolkit and applications for computational bio= logy" HOMEPAGE=3D"http://www.ncbi.nlm.nih.gov/" SRC_URI=3D" mirror://gentoo/${PN}-${PV/0./}.tar.gz doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )" # mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz ) LICENSE=3D"public-domain" SLOT=3D"0" KEYWORDS=3D"~alpha amd64 ~ppc ppc64 ~sparc x86" # IUSE=3D"doc mpi X" # mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi releas= e. # Currently seeking a fix. IUSE=3D"doc X" RDEPEND=3D"app-shells/tcsh dev-lang/perl media-libs/libpng X? ( >=3Dx11-libs/openmotif-2.3:0 )" DEPEND=3D"${RDEPEND} sys-devel/pmake" # mpi? ( virtual/mpi ) S=3D"${WORKDIR}/ncbi" EXTRA_VIB=3D"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 "${S}"/make sed -e "s:\#set HAVE_OGL=3D0:set HAVE_OGL=3D0:" \ -e "s:\#set HAVE_MOTIF=3D0:set HAVE_MOTIF=3D0:" \ -i makedis.csh || die else if use x86; then # X applications segfault on startup on x86 with -O3. replace-flags '-O3' '-O2' fi fi # Apply user C flags... cd "${S}"/platform # ... on x86... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3 -mcpu=3Dpentium4/NCBI_LDFLAGS1 =3D ${CFLAGS= }/" \ -e "s/NCBI_OPTFLAG =3D -O3 -mcpu=3Dpentium4/NCBI_OPTFLAG =3D ${CFLAGS}/= " \ -i linux-x86.ncbi.mk || die # ... on alpha... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3 -mieee/NCBI_LDFLAGS1 =3D -mieee ${CFLAGS}/"= \ -e "s/NCBI_OPTFLAG =3D -O3 -mieee/NCBI_OPTFLAG =3D -mieee ${CFLAGS}/" \ -i linux-alpha.ncbi.mk || die # ... on hppa... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O2/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O2/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i hppalinux.ncbi.mk || die # ... on ppc... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O2/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O2/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i ppclinux.ncbi.mk || die # ... on generic 64-bit Linux... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O3/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i linux64.ncbi.mk || die # ... on generic Linux. sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O3/NCBI_OPTFLAG =3D ${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 =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux-x86.ncbi.mk= || die # ... on alpha... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux-alpha.ncbi.= mk || die # ... on hppa... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" hppalinux.ncbi.mk= || die # ... on ppc... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" ppclinux.ncbi.mk = || die # ... on generic 64-bit Linux... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux64.ncbi.mk |= | die # ... on generic Linux. sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux.ncbi.mk || = die # We use dynamic libraries sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die # GNU make 3.81 is confused by those nightmarish Makefiles, so we use pm= ake # instead. The right solution would be to fix the Makefiles. (Be my gues= t.) cd "${S}"/make sed -i -e "s%CMD=3D'make%CMD=3D'/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=3D"-a" # eautoreconf # econf --with-ncbi=3D"${WORKDIR}"/ncbi --with-mpi=3D/usr # emake || die # fi } src_install() { dobin "${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=3D"${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentat= ion." # Developer documentation if use doc; then # Hypertext SDK documentation insinto /usr/share/doc/${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 "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config fil= e." # Env file to set the location of the config file and BLAST databases. newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env fil= e." } 1.1 sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ncbi-tools-0.20090809.ebuild?rev=3D1.1&view=3Dmarkup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-t= ools/ncbi-tools-0.20090809.ebuild?rev=3D1.1&content-type=3Dtext/plain Index: ncbi-tools-0.20090809.ebuild =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D # 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-0.20= 090809.ebuild,v 1.1 2012/06/13 10:49:23 jlec Exp $ EAPI=3D"2" inherit flag-o-matic toolchain-funcs eutils DESCRIPTION=3D"Development toolkit and applications for computational bio= logy, including NCBI BLAST" HOMEPAGE=3D"http://www.ncbi.nlm.nih.gov/" SRC_URI=3D"ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV/0./}/nc= bi.tar.gz -> ${P}.tar.gz" SLOT=3D"0" LICENSE=3D"public-domain" KEYWORDS=3D"~alpha amd64 ~ppc64 x86" # IUSE=3Dmpi deprecated, use sci-biology/mpiblast separately IUSE=3D"doc X" RDEPEND=3D"app-shells/tcsh dev-lang/perl media-libs/libpng X? ( >=3Dx11-libs/openmotif-2.3:0 )" DEPEND=3D"${RDEPEND}" S=3D"${WORKDIR}/ncbi" EXTRA_VIB=3D"asn2all asn2asn" pkg_setup() { echo ewarn 'Please note that the NCBI toolkit (and especially the X' ewarn 'applications) are known to have compilation and run-time' ewarn 'problems when compiled with agressive compilation flags. The' ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' ewarn 'X support is enabled.' echo } src_prepare() { epatch "${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=3D0:set HAVE_OGL=3D0:" \ -e "s:\#set HAVE_MOTIF=3D0:set HAVE_MOTIF=3D0:" \ -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 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3 -mcpu=3Dpentium4/NCBI_LDFLAGS1 =3D ${CFLAGS= }/" \ -e "s/NCBI_OPTFLAG =3D -O3 -mcpu=3Dpentium4/NCBI_OPTFLAG =3D ${CFLAGS}/= " \ -i linux-x86.ncbi.mk || die # ... on alpha... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3 -mieee/NCBI_LDFLAGS1 =3D -mieee ${CFLAGS}/"= \ -e "s/NCBI_OPTFLAG =3D -O3 -mieee/NCBI_OPTFLAG =3D -mieee ${CFLAGS}/" \ -i linux-alpha.ncbi.mk || die # ... on hppa... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O2/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O2/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i hppalinux.ncbi.mk || die # ... on ppc... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O2/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O2/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i ppclinux.ncbi.mk || die # ... on generic 64-bit Linux... sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O3/NCBI_OPTFLAG =3D ${CFLAGS}/" \ -i linux64.ncbi.mk || die # ... on generic Linux. sed -e "s/NCBI_CFLAGS1 =3D -c/NCBI_CFLAGS1 =3D -c ${CFLAGS}/" \ -e "s/NCBI_LDFLAGS1 =3D -O3/NCBI_LDFLAGS1 =3D ${CFLAGS}/" \ -e "s/NCBI_OPTFLAG =3D -O3/NCBI_OPTFLAG =3D ${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 =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux-x86.ncbi.mk= || die # ... on alpha... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux-alpha.ncbi.= mk || die # ... on hppa... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" hppalinux.ncbi.mk= || die # ... on ppc... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" ppclinux.ncbi.mk = || die # ... on generic 64-bit Linux... sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux64.ncbi.mk |= | die # ... on generic Linux. sed -i -e "s/NCBI_CC =3D gcc/NCBI_CC =3D $(tc-getCC)/" linux.ncbi.mk || = die # We use dynamic libraries sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die } src_compile() { export EXTRA_VIB cd "${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentat= ion." # Developer documentation if use doc; then # Demo programs mkdir "${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 fil= e." # Env file to set the location of the config file and BLAST databases. newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env fil= e." }