summaryrefslogtreecommitdiff
blob: 7bc4cb0cd59ab8dbf6eda71bbe9eebe3939a4353 (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
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild,v 1.4 2010/11/15 21:07:43 jlec Exp $

EAPI="3"

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 ~amd64-linux ~x86-linux ~ppc-macos"

# IUSE=mpi deprecated, use sci-biology/mpiblast separately
IUSE="doc X"

RDEPEND="app-shells/tcsh
	dev-lang/perl
	media-libs/libpng
	X? ( >=x11-libs/openmotif-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} ${LDFLAGS}/" \
		-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} ${LDFLAGS}/" \
		-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} ${LDFLAGS}/" \
		-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} ${LDFLAGS}/" \
		-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} ${LDFLAGS}/" \
		-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} ${LDFLAGS}/" \
		-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

	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
	mkdir "${S}"/real
	mv "${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 || die
	cp spidey ../bin/ || die
}

src_install() {
	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi #sci-geosciences/cdat-lite
	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 "${ED}"/usr/include/ncbi
	cp -RL "${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 "${S}"/{README,VERSION,doc/{*.txt,README.*}} || \
		die "Failed to install basic documentation."
	newdoc "${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 "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} || \
		die "Failed to install HTML documentation."
	insinto /usr/share/doc/${PF}/html/blast
	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
	insinto /usr/share/doc/${PF}/html/images
	doins "${S}"/doc/images/* || die "Failed to install documentation images."
	insinto /usr/share/doc/${PF}/html/seq_install
	doins "${S}"/doc/seq_install/* || die "Failed to install seq_install documentation."

	# 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/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."
}