+++ /dev/null
-# ChangeLog for app-sci/ncbi-tools
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/ncbi-tools/ChangeLog,v 1.19 2004/12/01 05:06:02 j4rg0n Exp $
-
- 30 Nov 2004; <j4rg0n@gentoo.org> ncbi-tools-20040616.ebuild:
- Keyworded ~ppc-macos.
-
- 22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org>
- ncbi-tools-20040616.ebuild:
- Added to ~amd64
-
- 14 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
- ncbi-tools-20040616.ebuild:
- Use gcc-getCC from gcc.eclass rather than ${CC}.
-
- 04 Oct 2004; Olivier Fisette <ribosome@gentoo.org>
- ncbi-tools-20040616.ebuild:
- Fixed potential bug in "SRC_URI".
-
-*ncbi-tools-20040616 (03 Oct 2004)
-
- 03 Oct 2004; Olivier Fisette <ribosome@gentoo.org> files/21ncbi,
- -files/dot-ncbirc, +files/ncbirc, -ncbi-tools-20031103.ebuild,
- -ncbi-tools-20040202-r1.ebuild, +ncbi-tools-20040616.ebuild:
- Updated version and new ebuild. This fixes bug #65941.
-
- 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> ncbi-tools-20031103.ebuild,
- ncbi-tools-20040202-r1.ebuild:
- Fix use invocation
-
- 05 May 2004; Bryan Østergaard <kloeri@gentoo.org>
- ncbi-tools-20040202-r1.ebuild:
- Stable on alpha.
-
- 19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org>
- ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
- ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
- ncbi-tools-20040202.ebuild:
- Cleanup, removing S=... with no effect
-
- 30 Mar 2004; Donnie Berkholz <spyderous@gentoo.org>;
- ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
- ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
- ncbi-tools-20040202.ebuild:
- Change x11-base/xfree dependency to virtual/x11.
-
- 21 Mar 2004; Martin Holzer <mholzer@gentoo.org>
- ncbi-tools-04222003-r2.ebuild, ncbi-tools-20030422.ebuild,
- ncbi-tools-20031103.ebuild, ncbi-tools-20040202-r1.ebuild,
- ncbi-tools-20040202.ebuild:
- adding categorie. see 45110 for details
-
-*ncbi-tools-20040202-r1 (06 Feb 2004)
-
- 06 Feb 2004; Stephen Diener <sediener@gentoo.org>
- ncbi-tools-20040202-r1.ebuild:
- Replaced buggy tarball with new one. Bumped revision to propogate.
-
-*ncbi-tools-20040202 (05 Feb 2004)
-
- 05 Feb 2004; Stephen Diener <sediener@gentoo.org>
- ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003.ebuild,
- ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild,
- ncbi-tools-20040202.ebuild:
- Bumped 20031103 to x86, removed old ebuilds, added new release 20040202
-
-*ncbi-tools-20040202 (04 Feb 2004)
-
- 04 Feb 2004; Stephen Diener <sediener@gentoo.org>
- ncbi-tools-20031103.ebuild, ncbi-tools-20040202.ebuild:
- Version bump. Changes -O3 -> -O2 so X11 apps will work.
-
- 11 Jan 2004; Heinrich Wendel <lanius@gentoo.org>
- ncbi-tools-04222003-r1.ebuild, ncbi-tools-04222003-r2.ebuild,
- ncbi-tools-20030422.ebuild, ncbi-tools-20031103.ebuild:
- fixed motif dep
-
-*ncbi-tools-20031103 (13 Dec 2003)
-
- 13 Dec 2003; Stephen Diener <sediener@gentoo.org>
- ncbi-tools-20031103.ebuild:
- Added november release of ncbi-tools (blast-2.2.6 included);
- Added support for -X
-
-*ncbi-tools-20030422 (11 Nov 2003)
-
- 11 Nov 2003; <sediener@gentoo.org> ncbi-tools-20030422.ebuild:
- added bl2seq to list of installed binaries; changed date format from 04222003
- to 20030422; renamed files to have date appended to not collide and changed
- SRC_URI to mirror://gentoo/
-
-*ncbi-tools-04222003-r2 (08 Oct 2003)
-
- 08 Oct 2003; Robin H. Johnson <robbat2@gentoo.org>
- ncbi-tools-04222003-r2.ebuild:
- modified patch from #30656, corrected two pathes in the postinst message
-
-*ncbi-tools-04222003-r1 (05 May 2003)
-
- 05 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003-r1.ebuild :
- A few enhancements from Gontran Zepeda <gontran@gontran.net>.
-
-*ncbi-tools-04222003 (03 May 2003)
-
- 03 May 2003; Jon Portnoy <avenj@gentoo.org> ncbi-tools-04222003 :
- Initial important. Ebuild submitted by Steve Diener
- <sediener@unity.ncsu.edu>.
+++ /dev/null
-# 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
-}
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