blob: 5a3f1ca33f32774df1b88b339b3b944dfb7dd1b0 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
# Copyright 1999-2015 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-r2.ebuild,v 1.7 2015/03/02 14:09:51 jlec Exp $
EAPI=5
inherit eutils flag-o-matic prefix toolchain-funcs
DESCRIPTION="Development toolkit and applications for computational biology, including NCBI BLAST"
HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
SLOT="0"
LICENSE="public-domain"
KEYWORDS="~alpha amd64 ppc64 x86 ~amd64-linux ~x86-linux ~ppc-macos"
IUSE="doc static-libs X"
RDEPEND="
app-shells/tcsh
dev-lang/perl
media-libs/libpng:0=
X? ( x11-libs/motif:0 )"
DEPEND="${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}"/${PN}-extra_vib.patch \
"${FILESDIR}"/${P}-bfr-overflow.patch \
"${FILESDIR}"/${P}-format-security.patch \
"${FILESDIR}"/${P}-_DEFAULT_SOURCE.patch
if use ppc || use ppc64; then
epatch "${FILESDIR}"/${PN}-lop.patch
fi
if ! use X; then
sed \
-e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \
-e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \
-i "${S}"/make/makedis.csh || die
else
# X applications segfault on startup on x86 with -O3.
use x86 || replace-flags '-O3' '-O2'
fi
# Apply user C flags...
cd "${S}"/platform
sed \
-e "s:-O[s0-9]\?::g" \
-e 's:-m\(cpu\|arch\)=[a-zA-Z0-9]*::g' \
-e 's:-x[A-Z]*::g' \
-e 's:-pipe::g' \
-e "/NCBI_MAKE_SHELL *=/s:=.*:= \"${EPREFIX}/bin/sh\":g" \
-e "/NCBI_AR *=/s:ar:$(tc-getAR):g" \
-e "/NCBI_RANLIB *=/s:ranlib:$(tc-getRANLIB):g" \
-e "/NCBI_CC *=/s:= [a-zA-Z0-9]* := $(tc-getCC) :g" \
-e "/NCBI_OPTFLAG *=/s:$: ${CFLAGS}:g" \
-e "/NCBI_LDFLAGS1 *=/s:$: ${CFLAGS} ${LDFLAGS}:g" \
-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --cflags gl glu 2>/dev/null):g" \
-e "/OPENGL_LIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-e "/NCBI_OGLLIBS *=/s:=.*:= $($(tc-getPKG_CONFIG) --libs gl glu 2>/dev/null):g" \
-i * || die
# We use dynamic libraries
sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
sed \
-re "s:/usr(/bin/.*sh):\1:g" \
-e "s:(/bin/.*sh):${EPREFIX}\1:g" \
-i $(find "${S}" -type f) || die
}
src_compile() {
export EXTRA_VIB
cd "${WORKDIR}"
csh ncbi/make/makedis.csh || die
mkdir "${S}"/cgi "${S}"/real || die
mv "${S}"/bin/*.cgi "${S}"/cgi || die
mv "${S}"/bin/*.REAL "${S}"/real || die
cd "${S}"/demo
emake \
-f ../make/makenet.unx \
CC="$(tc-getCC) ${CFLAGS} -I../include -L../lib" \
LDFLAGS="${LDFLAGS}" \
spidey
cp spidey ../bin/ || die
}
src_install() {
#sci-geosciences/cdat-lite
mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi || die
dobin "${S}"/bin/*
for i in ${EXTRA_VIB}; do
dobin "${S}"/build/${i} || die "Failed to install binaries."
done
use static-libs && dolib.a "${S}"/lib/*.a
mkdir -p "${ED}"/usr/include/ncbi
cp -RL "${S}"/include/* "${ED}"/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.*}}
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 "${S}"/sequin/README README.sequin
mv "${S}"/doc/man/fmerge{,-ncbi}.1 || die
doman "${S}"/doc/man/*
# Hypertext user documentation
dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}}
insinto /usr/share/doc/${PF}/html
doins -r "${S}"/doc/blast "${S}"/doc/images "${S}"/doc/seq_install
# Developer documentation
if use doc; then
# Demo programs
mkdir "${ED}"/usr/share/ncbi
mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
fi
# Shared data (similarity matrices and such) and database directory.
insinto /usr/share/ncbi
doins -r "${S}"/data
dodir /usr/share/ncbi/formatdb
# Default config file to set the path for shared data.
insinto /etc/ncbi
newins "${FILESDIR}"/ncbirc .ncbirc
eprefixify "${ED}"/etc/ncbi/.ncbirc
# Env file to set the location of the config file and BLAST databases.
newenvd "${FILESDIR}"/21ncbi-r1 21ncbi
}
|
GitWeb