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weaver 10/09/30 17:41:44 |
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|
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Modified: ChangeLog |
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Added: ncbi-tools-20100808.ebuild |
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Removed: ncbi-tools-20090809-r1.ebuild |
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Log: |
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Version bump |
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|
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(Portage version: 2.2_rc86/cvs/Linux x86_64) |
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|
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Revision Changes Path |
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1.79 sci-biology/ncbi-tools/ChangeLog |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.79&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?rev=1.79&content-type=text/plain |
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diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ChangeLog?r1=1.78&r2=1.79 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v |
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retrieving revision 1.78 |
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retrieving revision 1.79 |
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diff -u -r1.78 -r1.79 |
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--- ChangeLog 24 Jun 2010 20:41:40 -0000 1.78 |
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+++ ChangeLog 30 Sep 2010 17:41:44 -0000 1.79 |
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@@ -1,6 +1,12 @@ |
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# ChangeLog for sci-biology/ncbi-tools |
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# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.78 2010/06/24 20:41:40 jlec Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.79 2010/09/30 17:41:44 weaver Exp $ |
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+ |
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+*ncbi-tools-20100808 (30 Sep 2010) |
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+ |
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+ 30 Sep 2010; Andrey Kislyuk <weaver@g.o> |
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+ -ncbi-tools-20090809-r1.ebuild, +ncbi-tools-20100808.ebuild: |
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+ Version bump |
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|
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24 Jun 2010; Justin Lecher <jlec@g.o> -ncbi-tools-20060507.ebuild, |
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-ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild, |
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|
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|
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|
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1.1 sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: ncbi-tools-20100808.ebuild |
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=================================================================== |
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# Copyright 1999-2010 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild,v 1.1 2010/09/30 17:41:44 weaver Exp $ |
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|
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EAPI="3" |
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|
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inherit flag-o-matic toolchain-funcs eutils |
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|
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DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST" |
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LICENSE="public-domain" |
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HOMEPAGE="http://www.ncbi.nlm.nih.gov/" |
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SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz -> ${P}.tar.gz" |
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|
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SLOT="0" |
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KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" |
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|
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# IUSE=mpi deprecated, use sci-biology/mpiblast separately |
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IUSE="doc X" |
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|
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RDEPEND="app-shells/tcsh |
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dev-lang/perl |
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media-libs/libpng |
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X? ( x11-libs/openmotif )" |
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DEPEND="${RDEPEND}" |
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|
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S="${WORKDIR}/ncbi" |
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|
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EXTRA_VIB="asn2all asn2asn" |
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|
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pkg_setup() { |
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echo |
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ewarn 'Please note that the NCBI toolkit (and especially the X' |
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ewarn 'applications) are known to have compilation and run-time' |
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ewarn 'problems when compiled with agressive compilation flags. The' |
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ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' |
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ewarn 'X support is enabled.' |
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echo |
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} |
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|
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src_prepare() { |
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epatch "${FILESDIR}"/${PN}-extra_vib.patch |
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|
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if use ppc || use ppc64; then |
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epatch "${FILESDIR}"/${PN}-lop.patch |
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fi |
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|
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if ! use X; then |
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cd "${S}"/make |
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sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ |
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-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ |
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-i makedis.csh || die |
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else |
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if use x86; then |
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# X applications segfault on startup on x86 with -O3. |
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replace-flags '-O3' '-O2' |
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fi |
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fi |
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|
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# Apply user C flags... |
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cd "${S}"/platform |
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# ... on x86... |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \ |
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-i linux-x86.ncbi.mk || die |
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# ... on alpha... |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \ |
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-i linux-alpha.ncbi.mk || die |
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# ... on hppa... |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ |
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-i hppalinux.ncbi.mk || die |
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# ... on ppc... |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ |
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-i ppclinux.ncbi.mk || die |
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# ... on generic 64-bit Linux... |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \ |
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-i linux64.ncbi.mk || die |
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# ... on generic Linux. |
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sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ |
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-e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS} ${LDFLAGS}/" \ |
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-e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \ |
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-i linux.ncbi.mk || die |
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|
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# Put in our MAKEOPTS (doesn't work). |
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# sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh |
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|
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# Set C compiler... |
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# ... on x86... |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die |
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# ... on alpha... |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die |
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# ... on hppa... |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die |
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# ... on ppc... |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die |
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# ... on generic 64-bit Linux... |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die |
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# ... on generic Linux. |
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sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die |
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|
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# We use dynamic libraries |
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sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die |
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} |
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|
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src_compile() { |
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export EXTRA_VIB |
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cd "${WORKDIR}" |
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ncbi/make/makedis.csh || die |
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mkdir "${S}"/cgi |
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mkdir "${S}"/real |
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mv "${S}"/bin/*.cgi "${S}"/cgi || die |
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mv "${S}"/bin/*.REAL "${S}"/real || die |
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cd "${S}"/demo |
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emake \ |
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-f ../make/makenet.unx \ |
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CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \ |
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LDFLAGS="${LDFLAGS}" \ |
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spidey || die |
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cp spidey ../bin/ || die |
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} |
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|
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src_install() { |
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mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi #sci-geosciences/cdat-lite |
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dobin "${S}"/bin/* || die "Failed to install binaries." |
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for i in ${EXTRA_VIB}; do |
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dobin "${S}"/build/${i} || die "Failed to install binaries." |
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done |
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dolib "${S}"/lib/* || die "Failed to install libraries." |
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mkdir -p "${ED}"/usr/include/ncbi |
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cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \ |
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die "Failed to install headers." |
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|
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# TODO: wwwblast with webapps |
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#insinto /usr/share/ncbi/lib/cgi |
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#doins ${S}/cgi/* |
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#insinto /usr/share/ncbi/lib/real |
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#doins ${S}/real/* |
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|
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# Basic documentation |
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dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} || \ |
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die "Failed to install basic documentation." |
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newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \ |
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die "Failed renaming fa2htgs documentation." |
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newdoc "${S}"/config/README README.config || \ |
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die "Failed renaming config documentation." |
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newdoc "${S}"/network/encrypt/README README.encrypt || \ |
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die "Failed renaming encrypt documentation." |
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newdoc "${S}"/network/nsclilib/readme README.nsclilib || \ |
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die "Failed renaming nsclilib documentation." |
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newdoc "${S}"/sequin/README README.sequin || \ |
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die "Failed renaming sequin documentation." |
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doman "${S}"/doc/man/* || \ |
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die "Failed to install man pages." |
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|
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# Hypertext user documentation |
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dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} || \ |
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die "Failed to install HTML documentation." |
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insinto /usr/share/doc/${PF}/html/blast |
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doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation." |
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insinto /usr/share/doc/${PF}/html/images |
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doins "${S}"/doc/images/* || die "Failed to install documentation images." |
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insinto /usr/share/doc/${PF}/html/seq_install |
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doins "${S}"/doc/seq_install/* || die "Failed to install seq_install documentation." |
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|
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# Developer documentation |
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if use doc; then |
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# Demo programs |
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mkdir "${ED}"/usr/share/ncbi |
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mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die |
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fi |
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|
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# Shared data (similarity matrices and such) and database directory. |
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insinto /usr/share/ncbi/data |
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doins "${S}"/data/* || die "Failed to install shared data." |
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dodir /usr/share/ncbi/formatdb || die |
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|
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# Default config file to set the path for shared data. |
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insinto /etc/ncbi |
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newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file." |
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|
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# Env file to set the location of the config file and BLAST databases. |
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newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file." |
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} |
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