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-rw-r--r--sci-biology/ncbi-tools/ChangeLog10
-rw-r--r--sci-biology/ncbi-tools/metadata.xml10
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild8
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild8
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild5
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild222
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild179
7 files changed, 26 insertions, 416 deletions
diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 26cc14f56f53..b74895569524 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
# 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 1.86 2012/10/24 19:31:33 ulm Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.87 2013/02/18 12:53:27 jlec Exp $
+
+ 18 Feb 2013; Justin Lecher <jlec@gentoo.org> ncbi-tools-0.20080302.ebuild,
+ ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild,
+ -ncbi-tools-20080302.ebuild, -ncbi-tools-20090809.ebuild, metadata.xml:
+ Drop old; rename fmerge.1 to fmerg-ncbi.1 -> resolves collision with
+ dev-util/fhist, #429560
24 Oct 2012; Ulrich Müller <ulm@gentoo.org> ncbi-tools-0.20080302.ebuild,
ncbi-tools-0.20090809.ebuild, ncbi-tools-2.2.26.ebuild,
diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/ncbi-tools/metadata.xml
+++ b/sci-biology/ncbi-tools/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
index ed292e2f2873..6d354f01c39f 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild,v 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20080302.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
EAPI=1
@@ -24,8 +24,10 @@ KEYWORDS="~alpha amd64 ~ppc ppc64 ~sparc x86"
IUSE="doc X"
-RDEPEND="app-shells/tcsh
+RDEPEND="
+ app-shells/tcsh
dev-lang/perl
+ !dev-util/fhist
media-libs/libpng
X? ( >=x11-libs/motif-2.3:0 )"
diff --git a/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
index 2d3c2dfd5c12..16c94b205bde 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild,v 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-0.20090809.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
EAPI="2"
@@ -17,8 +17,10 @@ KEYWORDS="~alpha amd64 ~ppc64 x86"
# IUSE=mpi deprecated, use sci-biology/mpiblast separately
IUSE="doc X"
-RDEPEND="app-shells/tcsh
+RDEPEND="
+ app-shells/tcsh
dev-lang/perl
+ !dev-util/fhist
media-libs/libpng
X? ( >=x11-libs/motif-2.3:0 )"
DEPEND="${RDEPEND}"
diff --git a/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
index 14fbd62bec8e..bc6bc16b9064 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild,v 1.2 2012/10/24 19:31:33 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-2.2.26.ebuild,v 1.3 2013/02/18 12:53:27 jlec Exp $
EAPI=4
@@ -121,6 +121,7 @@ src_install() {
newdoc "${S}"/network/encrypt/README README.encrypt
newdoc "${S}"/network/nsclilib/readme README.nsclilib
newdoc "${S}"/sequin/README README.sequin
+ mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
doman "${S}"/doc/man/*
# Hypertext user documentation
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
deleted file mode 100644
index a00a280cac3b..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild
+++ /dev/null
@@ -1,222 +0,0 @@
-# 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-20080302.ebuild,v 1.9 2012/10/24 19:31:33 ulm Exp $
-
-EAPI=1
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications 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 )"
-
-# mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz )
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc ppc64 ~sparc x86"
-
-# IUSE="doc mpi X"
-# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release.
-# Currently seeking a fix.
-
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
- dev-lang/perl
- media-libs/libpng
- X? ( >=x11-libs/motif-2.3:0 )"
-
-DEPEND="${RDEPEND}
- sys-devel/pmake"
-
-# mpi? ( virtual/mpi )
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="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 "${S}"/make
- sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
- -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
- -i makedis.csh || die
- else
- if use x86; then
- # X applications segfault on startup on x86 with -O3.
- replace-flags '-O3' '-O2'
- fi
- fi
-
- # Apply user C flags...
- cd "${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 64-bit 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 linux64.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 64-bit Linux...
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
- # ... on generic Linux.
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
- # We use dynamic libraries
- sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-
- # GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
- # instead. The right solution would be to fix the Makefiles. (Be my guest.)
- cd "${S}"/make
- sed -i -e "s%CMD='make%CMD='/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="-a"
-# eautoreconf
-# econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr
-# emake || die
-# fi
-}
-
-src_install() {
- dobin "${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="${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
- # Developer documentation
- if use doc; then
- # Hypertext SDK documentation
- insinto /usr/share/doc/${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 "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file."
-
- # Env file to set the location of the config file and BLAST databases.
- newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
deleted file mode 100644
index a744b4572c04..000000000000
--- a/sci-biology/ncbi-tools/ncbi-tools-20090809.ebuild
+++ /dev/null
@@ -1,179 +0,0 @@
-# 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-20090809.ebuild,v 1.6 2012/10/24 19:31:33 ulm Exp $
-
-EAPI="2"
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 x86"
-
-# IUSE=mpi deprecated, use sci-biology/mpiblast separately
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
- dev-lang/perl
- media-libs/libpng
- X? ( >=x11-libs/motif-2.3:0 )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/ncbi"
-
-EXTRA_VIB="asn2all asn2asn"
-
-pkg_setup() {
- echo
- ewarn 'Please note that the NCBI toolkit (and especially the X'
- ewarn 'applications) are known to have compilation and run-time'
- ewarn 'problems when compiled with agressive compilation flags. The'
- ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if'
- ewarn 'X support is enabled.'
- echo
-}
-
-src_prepare() {
- epatch "${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=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 64-bit 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 linux64.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 64-bit Linux...
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die
- # ... on generic Linux.
- sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
-
- # We use dynamic libraries
- sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-}
-
-src_compile() {
- export EXTRA_VIB
- cd "${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
- # Developer documentation
- if use doc; then
- # Demo programs
- mkdir "${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 file."
-
- # Env file to set the location of the config file and BLAST databases.
- newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file."
-}