diff options
Diffstat (limited to 'app-sci/ncbi-tools/ncbi-tools-20040616.ebuild')
| -rw-r--r-- | app-sci/ncbi-tools/ncbi-tools-20040616.ebuild | 165 |
1 files changed, 0 insertions, 165 deletions
diff --git a/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild b/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild deleted file mode 100644 index 0c4d333cd6ba..000000000000 --- a/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2004 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ncbi-tools-20040616.ebuild,v 1.5 2004/12/01 05:06:02 j4rg0n Exp $ - -inherit flag-o-matic gcc - -DESCRIPTION="Development toolkit and applications (BLAST, entrez, ddv, udv, sequin...) 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 )" - -SLOT="0" -KEYWORDS="~x86 ~ppc ~sparc ~alpha ~amd64 ~ppc-macos" -IUSE="doc X" - -DEPEND="app-shells/tcsh - dev-lang/perl - media-libs/libpng - X? ( virtual/x11 - x11-libs/openmotif - )" - -S=${WORKDIR}/ncbi - -pkg_setup() { - echo - ewarn 'It is important to note that the NCBI tools (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. If you experience difficulties with this' - ewarn 'package and use agressive "CFLAGS", lower the "CFLAGS" and try' - ewarn 'to install the NCBI tools again.' - echo -} - -src_unpack() { - unpack ${A} - - if ! use X; then - cd ${S}/make - sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" -i makedis.csh - sed -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" -i makedis.csh - 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 -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux-x86.ncbi.mk - sed -i -e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentiumpro/NCBI_LDFLAGS1 = ${CFLAGS}/" linux-x86.ncbi.mk - sed -i -e "s/NCBI_OPTFLAG = -O3 -mcpu=pentiumpro/NCBI_OPTFLAG = ${CFLAGS}/" linux-x86.ncbi.mk - # ... on alpha... - sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux-alpha.ncbi.mk - sed -i -e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" linux-alpha.ncbi.mk - sed -i -e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" linux-alpha.ncbi.mk - # ... on hppa... - sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" hppalinux.ncbi.mk - sed -i -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" hppalinux.ncbi.mk - sed -i -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" hppalinux.ncbi.mk - # ... on ppc... - sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" ppclinux.ncbi.mk - sed -i -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" ppclinux.ncbi.mk - sed -i -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" ppclinux.ncbi.mk - # ... on generic Linux. - sed -i -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" linux.ncbi.mk - sed -i -e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" linux.ncbi.mk - sed -i -e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" linux.ncbi.mk - - # 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 = $(gcc-getCC)/" linux-x86.ncbi.mk - # ... on alpha... - sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" linux-alpha.ncbi.mk - # ... on hppa... - sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" hppalinux.ncbi.mk - # ... on ppc... - sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" ppclinux.ncbi.mk - # ... on generic Linux. - sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(gcc-getCC)/" linux.ncbi.mk -} - -src_compile() { - cd ${WORKDIR} - ncbi/make/makedis.csh || die - mkdir ${S}/cgi - mkdir ${S}/real - mv ${S}/bin/*.cgi ${S}/cgi - mv ${S}/bin/*.REAL ${S}/real -} - -src_install() { - dobin ${S}/bin/* - dolib ${S}/lib/* - mkdir -p ${D}/usr/include/ncbi - cp -RL ${S}/include/* ${D}/usr/include/ncbi - - # 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}} - 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 - doman ${S}/doc/man/* - - # Hypertext user documentation - dohtml ${S}/{README.html,doc/{*.html *.gif}} - insinto /usr/share/doc/${PF}/html/blast - doins ${S}/doc/blast/* - - # Developer documentation - if use doc; then - # "socks" documentation - SOCKS="network/socks/socks.cstc.4.2" - insinto /usr/share/doc/${PF}/socks - doins ${S}/${SOCKS}/{CHANGES,How_to_SOCKSify,README.{1st,4.{0,1,2},DK},What_are_the_risks,What_SOCKS_expects} - newins ${S}/${SOCKS}/libident/README README.libident - doins ${S}/${SOCKS}/sockd/sockd.conf.sample - doman ${S}/${SOCKS}/{doc/*.{1,5,8},libident/ident.3} - # "regexp" documentation - insinto /usr/share/doc/${PF}/regexp - doins ${S}/regexp/doc/{AUTHORS,NEWS,README,Tech.Notes,*.txt} - insinto /usr/share/doc/${PF}/regexp/html - doins ${S}/regexp/doc/*.html - doman ${S}/regexp/doc/*.{1,3} - # Hypertext SDK documentation - insinto /usr/share/doc/${PF}/html/sdk - doins ${WORKDIR}/${PN}-sdk-doc/* - # Demo programs - mkdir ${D}/usr/share/ncbi - mv ${S}/demo ${D}/usr/share/ncbi/demo - mv ${S}/regexp/demo ${D}/usr/share/ncbi/demo/regexp - mv ${S}/regexp/test ${D}/usr/share/ncbi/demo/regexp/test - fi - - # Shared data (similarity matrices and such) and database directory. - insinto /usr/share/ncbi/data - doins ${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. - dodir /etc/env.d - insinto /etc/env.d - doins ${FILESDIR}/21ncbi -} |