# ChangeLog for sci-biology/ncbi-tools
# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.30 2005/10/22 16:02:56 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.31 2005/10/22 17:45:46 ribosome Exp $
+
+ 22 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -files/21ncbi,
+ -ncbi-tools-20041020-r1.ebuild, -ncbi-tools-20050429.ebuild:
+ Pruning old versions.
22 Oct 2005; Fabian Groffen <grobian@gentoo.org>
ncbi-tools-20050605.ebuild:
-MD5 6c8b57dc3b8c8523ae2adb7a1a8f1ed3 ncbi-tools-20041020-r1.ebuild 5630
MD5 be21ba792698dcaa322cfa98371eadf3 ncbi-tools-20050605.ebuild 5690
-MD5 0cfe991ee8c23a5a862c2386eba988e8 ncbi-tools-20050429.ebuild 5628
-MD5 7d3a037a19b037aff42ab423fabe2a9a ChangeLog 7941
+MD5 3b3a6c467e5443baabdce9d6dec4fd8b ChangeLog 8098
MD5 f189a3c4ff5ae55bcee4f8ed0ace5d20 metadata.xml 254
MD5 23986a001c85eb8c2c319aacfa9cb40c files/ncbirc 33
-MD5 6fa8c1b5254e9c217c399c949bc75f45 files/digest-ncbi-tools-20041020-r1 144
-MD5 ae77b2436a5f4dfcb6f71f2149782dc7 files/digest-ncbi-tools-20050429 144
MD5 9cef4ca17113d005c44d3bf3d330f747 files/digest-ncbi-tools-20050605 144
MD5 a5f54430f6f7422d75320e91068cae0b files/21ncbi-r1 232
-MD5 756db6700c84d3b303bfc3d0a28871de files/21ncbi 166
MD5 6b62beda180ee6d7d4d4a52507acc3ff files/ncbi-tools-20050605-lop.patch 701
+++ /dev/null
-# Location of the formatdb data sets
-BLASTDB="/usr/share/ncbi/formatdb"
-# Location of the ".ncbi.rc" file which sets the default path for shared data.
-NCBI=/etc/ncbi
+++ /dev/null
-MD5 3f82bce2a3ce549f055ff989a4b825ed ncbi-tools-20041020.tar.gz 13867811
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
+++ /dev/null
-MD5 f814c7b8b433cc479d5aa783a61e21c8 ncbi-tools-20050429.tar.gz 14061320
-MD5 c0860f787d95623b72fba58dbf1b60c5 ncbi-tools-sdk-doc.tar.bz2 263568
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20041020-r1.ebuild,v 1.5 2005/06/09 10:16:21 corsair Exp $
-
-inherit flag-o-matic toolchain-funcs
-
-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="~alpha ~amd64 ppc ppc-macos ppc64 ~sparc x86"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
- dev-lang/perl
- media-libs/libpng
- X? ( virtual/x11
- virtual/motif
- )"
-
-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:" \
- -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=pentiumpro/NCBI_LDFLAGS1 = ${CFLAGS}/" \
- -e "s/NCBI_OPTFLAG = -O3 -mcpu=pentiumpro/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 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 Linux.
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-}
-
-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.
- newenvd ${FILESDIR}/21ncbi-r1 21ncbi
-}
+++ /dev/null
-# Copyright 1999-2005 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20050429.ebuild,v 1.7 2005/09/16 07:19:58 agriffis Exp $
-
-inherit flag-o-matic toolchain-funcs
-
-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="alpha ~amd64 -ppc ~ppc-macos -ppc64 ~sparc x86"
-IUSE="doc X"
-
-DEPEND="app-shells/tcsh
- dev-lang/perl
- media-libs/libpng
- X? ( virtual/x11
- virtual/motif
- )"
-
-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:" \
- -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 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 Linux.
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-}
-
-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.
- newenvd ${FILESDIR}/21ncbi-r1 21ncbi
-}
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