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
|
# 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 1.5 2005/08/08 22:52:46 ranger 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
}
|
GitWeb