blob: b56d2699923369947a8f680735afffc9021f6d33 (
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
|
# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-pkg-simple prefix python-r1 versionator
MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
MY_PATCH="20120106"
MY_P="${PN}-v${MY_PV}-linux"
DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins"
HOMEPAGE="http://shiftx2.wishartlab.com/"
SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
SLOT="0"
LICENSE="all-rights-reserved"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE="debug"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
CDEPEND="dev-util/weka ${PYTHON_DEPS}"
RDEPEND="${CDEPEND}
${PYTHON_DEPS}
dev-lang/R
sci-biology/ncbi-tools
sci-chemistry/reduce
>=virtual/jre-1.5"
DEPEND="${CDEPEND}
>=virtual/jdk-1.5"
S="${WORKDIR}"/${MY_P}
QA_PREBUILT="/opt/.*"
src_prepare() {
epatch \
"${FILESDIR}"/${P}-java.patch \
"${FILESDIR}"/${P}-system.patch \
"${FILESDIR}"/${P}-internal-name.patch \
"${FILESDIR}"/${P}-format-security.patch
rm "${S}"/src/FeatureRanges.java || die
shared=$(echo "${EPREFIX}/usr/share/${PN}" | sed -e 's/\//\\\//g')
sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die
if use debug; then
sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die
fi
# hack alert!
sed \
-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
-i modules/*/Makefile || die
sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
eprefixify ${PN}.py
}
src_compile() {
mkdir "${S}"/build || die
ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
-d "${S}"/build $(find src/ -name "*.java")
jar cf "${PN}.jar" -C "${S}"/build . || die
einfo "Building module angles"
cd "${S}"/modules/angles || die
emake clean
emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi
einfo "Building module resmf"
cd "${S}"/modules/resmf || die
emake clean
emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf
einfo "Building module effects"
cd "${S}"/modules/effects || die
emake clean
emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
}
src_install() {
java-pkg_dojar "${PN}.jar"
java-pkg_dolauncher j${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin"
insinto /usr/share/${PN}
doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff}
doins -r "${S}"/lib/predmodels
insinto /usr/share/${PN}/vader
doins -r "${S}"/modules/resmf/lib/*
local instdir="/opt/${PN}"
dodoc README 1UBQ.pdb
python_foreach_impl python_newscript ${PN}.py ${PN}
mv shiftx2_util.py shiftx2util.py || die
python_moduleinto ${PN}
touch __init__.py
python_foreach_impl python_domodule natsorted.py shiftx2util.py __init__.py
# other modules
dobin \
"${S}"/modules/angles/{get_angles,phipsi} \
"${S}"/modules/resmf/resmf \
"${S}"/modules/effects/caleffect
# script
python_foreach_impl python_doscript "${S}"/script/*py
exeinto ${instdir}/script
doexe "${S}"/script/*.r
# shifty3
python_foreach_impl python_newscript "${S}"/shifty3/*py shifty3
exeinto ${instdir}/shifty3
doexe "${S}"/shifty3/xalign_x
dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
insinto ${instdir}/shifty3
doins -r "${S}"/shifty3/{blastdb,refdb,xalign.parms,wt.rbo}
python_foreach_impl python_doscript "${S}"/shifty3/utils/*py
dobin "${S}"/shifty3/utils/create_blastdb.sh
}
|
GitWeb