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
197
198
199
200
|
# Copyright 1999-2004 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/app-sci/staden/staden-1.4.1-r4.ebuild,v 1.1 2004/09/16 23:13:26 ribosome Exp $
inherit eutils
DESCRIPTION="The Staden Package - Biological sequence handling and analysis"
HOMEPAGE="http://${PN}.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${PN}-src-rel-${PV//./-}.tar.gz
mirror://gentoo/${P}-doc.tar.bz2
doc? mirror://gentoo/${P}-course.tar.bz2"
LICENSE="${PN}"
SLOT="0"
KEYWORDS="~x86"
IUSE="doc emboss ifc"
DEPEND="${RDEPEND}
dev-lang/perl
ifc? ( dev-lang/ifc )"
RDEPEND="app-shells/ksh
dev-lang/tcl
dev-lang/tk
=dev-tcltk/itcl-3.2*
dev-tcltk/iwidgets
media-libs/libpng
virtual/x11"
PDEPEND="emboss? ( app-sci/staden-emboss )"
S=${WORKDIR}/${PN}-src-rel-${PV//./-}
pkg_setup() {
# Check for a Fortran compiler.
if ! which ${F77:-g77} &> /dev/null; then
echo
eerror "The Fortran compiler \"${F77:-g77}\" could not be found on your system."
if [ -z ${F77} ] || [ ${F77} = g77 ]; then
eerror 'Please reinstall "sys-devel/gcc" with the "f77" "USE" flag enabled.'
elif [ ${F77} = ifc ] && ! use ifc &> /dev/null; then
eerror 'Please set the "ifc" "USE" flag if you want to use the Intel Fortran'
eerror 'Compiler to build this package. This will ensure the "dev-lang/ifc"'
eerror 'package gets installed on your system.'
elif [ ${F77} = ifc ] && use ifc &> /dev/null; then
eerror 'Please ensure "ifc" is in a directory referenced in "PATH".'
else
eerror 'Please make sure the variable ${F77} is set to the name of a valid'
eerror 'Fortran compiler installed on your system. Make sure this executable'
eerror 'is in a directory referenced by "PATH", and that the corresponding'
eerror '"USE" flag is set if applicable (for example "ifc" if you use the'
eerror 'Intel Fortran Compiler).'
fi
die "Fortran compiler not found."
fi
}
src_unpack() {
unpack ${A}
# The following Makefiles are more or less broken. Libraries are missing,
# or their directories are not included, or the variables are not set
# correctly and must be replaced by hardcoded library names. The
# top-level Makefile is also changed to avoid compiling documentation
# (which is provided prebuilt because of numerous compilation/dead links
# problems).
cd ${S}
einfo "Patching Staden Package Makefiles:"
epatch ${FILESDIR}/${P}-top.patch
epatch ${FILESDIR}/${P}-gap4.patch
epatch ${FILESDIR}/${P}-mutscan.patch
epatch ${FILESDIR}/${P}-prefinish.patch
epatch ${FILESDIR}/${P}-tk_utils.patch
epatch ${FILESDIR}/${P}-tracediff.patch
echo
# "getopt" is incorrectly included as an extern (for Win32 compatibility).
einfo "Patching Staden Package code:"
epatch ${FILESDIR}/${P}-getopt.patch
echo
# "CFLAGS" and "FFLAGS" need to be set to the user's values in the build
# system global Makefile.
einfo "Applying user-defined compilation/linking flags:"
cd ${S}/src/mk
sed -i -e "s/COPT = -O2 -g3 -DNDEBUG/COPT = ${CFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
&& einfo "Successfully applied sed script to set CFLAGS." \
|| eerror "Failed to apply sed script to set CFLAGS."
sed -i -e "s/FOPT = -O2 -g3 -DNDEBUG/FOPT = ${FFLAGS:-"-O2 -g3 -DNDEBUG"}/" global.mk \
&& einfo "Successfully applied sed script to set FFLAGS." \
|| eerror "Failed to apply sed script to set FFLAGS."
}
src_compile() {
# "MACHINE", "{STADEN,SRC}ROOT" and "JOB" are mandatory arguments to the
# Staden Package build process. "O" is redefined on the command line to
# avoid a conflict between Portage and the Staden Package build system,
# which both use this variable. (In Portage, its value is the directory
# containing the current ebuild, while in the Staden Package build system
# it is set to the directory containing the compiler object files.)
# Compiler program names also need to be specified to override the
# incorrect hardcoded ones.
# Compiles executables and libraries.
make \
STADENROOT="${S}" \
SRCROOT="${S}/src" \
MACHINE="linux" \
JOB="all" \
O="linux-binaries" \
CC=${CC:-gcc} \
CXX=${CXX:-g++} \
F77=${F77:-g77} \
|| die "Package compilation failed."
# Moves executables in "${S}/linux-bin" and libraries to ${S}/lib.
make \
STADENROOT="${S}" \
SRCROOT="${S}/src" \
MACHINE="linux" \
JOB="all" \
O="linux-binaries" \
install || die "Package pre-installation failed."
# Remove Makefiles from directories which will be manually installed.
rm ${S}/lib/Makefile
rm ${S}/demo/Makefile
rm ${S}/tables/Makefile
rm ${S}/userdata/Makefile
# Remove trashed "linux-binaries" file and replace it by a directory
# containing the appropriate libraries.
rm ${S}/lib/linux-binaries
mkdir ${S}/lib/linux-binaries
mv ${S}/src/lib/linux-binaries/* ${S}/lib/linux-binaries
ln -s /usr/lib/libitcl3.2.so ${S}/lib/itcl3.3/libitcl3.3.so
ln -s /usr/lib/libitk3.2.so ${S}/lib/itk3.3/libitk3.3.so
cp ${FILESDIR}/${P}-iwidgetsrc.new ${S}/tables/iwidgetsrc
epatch ${FILESDIR}/${P}-emboss.patch
# Netscape is not a good default browser (security masked in Portage).
# Use documentation.html rather than staden_home.html as the top-level
# hypertext documentation file.
cp ${FILESDIR}/${P}-staden_help.new ${S}/linux-bin/staden_help
chmod +x ${S}/linux-bin/staden_help
# Remove the prebuilt EMBOSS tcl/tk GUIs.
rm ${S}/tables/emboss_menu
rm -r ${S}/lib/spin2_emboss/acdtcl
}
src_install() {
# Executables and libraries
into /opt/${PN}
mkdir -p ${D}/opt/${PN}
mv ${S}/linux-bin ${D}/opt/${PN}/linux-bin
mv ${S}/lib ${D}/opt/${PN}/lib
# Shared files
mv ${S}/demo ${D}/opt/${PN}
mv ${S}/tables ${D}/opt/${PN}
mv ${S}/userdata ${D}/opt/${PN}
# "env" file for setting paths to Staden Package root, libraries, tables...
insinto /etc/env.d
newins ${FILESDIR}/${P}-env 27${PN}
# Man pages
doman ${S}/doc/manual/man/man*/*
# Documentation
mv ${WORKDIR}/doc ${D}/opt/${PN}/doc
# A short course in printable format along with some data
use doc && mv ${WORKDIR}/course ${D}/opt/${PN}/course
}
pkg_postinst() {
echo
ewarn 'Known issues:'
ewarn
ewarn 'The help browser integrated in the GUI applications reports missing'
ewarn 'files when following hyperlinks on the main documentation page. This'
ewarn 'seems to be a problem in the Staden Package help browser. You might'
ewarn 'want to use your favorite browser instead of the integrated one to'
ewarn 'read the documentation.'
ewarn
ewarn 'The GUI programs may crash when bringing up the font selection'
ewarn 'dialog. This problem is related to the presence of certain'
ewarn 'fonts in "FontPath". If you experience this problem, try using'
ewarn '"strace" to identify the problematic font(s) and either uninstall'
ewarn 'them or remove the directory they are in from "FontPath" by'
ewarn 'editing your X server configuration file.'
echo
}
|
GitWeb