Gentoo Archives: gentoo-commits

From: Anna Vyalkova <cyber+gentoo@×××××.in>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] repo/proj/guru:dev commit in: sci-biology/geneathome/files/, sci-biology/geneathome/
Date: Wed, 19 May 2021 01:06:25
Message-Id: 1621386366.0b33cc8749ef3a099e2db52b2f273a602d811fbd.cybertailor@gentoo
1 commit: 0b33cc8749ef3a099e2db52b2f273a602d811fbd
2 Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in>
3 AuthorDate: Wed May 19 01:06:06 2021 +0000
4 Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in>
5 CommitDate: Wed May 19 01:06:06 2021 +0000
6 URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=0b33cc87
7
8 sci-biology/geneathome: initial import
9
10 Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in>
11
12 sci-biology/geneathome/Manifest | 2 +
13 sci-biology/geneathome/files/app_config.xml | 20 +++++++
14 sci-biology/geneathome/files/makefile.patch | 44 +++++++++++++++
15 sci-biology/geneathome/geneathome-1.10.ebuild | 78 +++++++++++++++++++++++++++
16 sci-biology/geneathome/metadata.xml | 11 ++++
17 5 files changed, 155 insertions(+)
18
19 diff --git a/sci-biology/geneathome/Manifest b/sci-biology/geneathome/Manifest
20 new file mode 100644
21 index 000000000..5a086b395
22 --- /dev/null
23 +++ b/sci-biology/geneathome/Manifest
24 @@ -0,0 +1,2 @@
25 +DIST boinc-7.16.16.tar.gz 49599131 BLAKE2B 819ab85c19a684144711f77e669b892aa73c006b81c1d7ef7adbd9d580e1e8473ae27b52dc17953ee677c70fc78ed15df936afd740e629715f30f2b81d84ea6f SHA512 dd7042e176d6506c70de7866556ae73b2f45734df92038086d5b0414751f3da08dc571c49f0c26d747d3fb2577674d3ff8cdec7d3563861eaaaa5af9c1db0a0e
26 +DIST geneathome-1.10.tar.gz 73686241 BLAKE2B 4a4e9930e3faeaf0b6d687d26adb3267af1a70096397e9e4001066a7029a854b95cd35b6779a0e6bcf6c9cb3ad662b5f9e6adf4ab9d608ed2d73c65d3dadc10b SHA512 c8c1bb65f0021d9c9d9f14375212c458694dbb21abbfa90f6b8fb958bc6d86a522bbe13846b5930f6df0a4e755256f2016c5edd4447ae147cb1381eccce06b9e
27
28 diff --git a/sci-biology/geneathome/files/app_config.xml b/sci-biology/geneathome/files/app_config.xml
29 new file mode 100644
30 index 000000000..43b80156b
31 --- /dev/null
32 +++ b/sci-biology/geneathome/files/app_config.xml
33 @@ -0,0 +1,20 @@
34 +<app_info>
35 +<app>
36 + <name>gene_pcim</name>
37 + <user_friendly_name>gene@home PC-IM</user_friendly_name>
38 +</app>
39 +
40 +<file_info>
41 + <name>gene_pcim_v1.10</name>
42 + <executable/>
43 +</file_info>
44 +
45 +<app_version>
46 + <app_name>gene_pcim</app_name>
47 + <version_num>110</version_num>
48 + <file_ref>
49 + <file_name>gene_pcim_v1.10</file_name>
50 + <main_program/>
51 + </file_ref>
52 +</app_version>
53 +</app_info>
54
55 diff --git a/sci-biology/geneathome/files/makefile.patch b/sci-biology/geneathome/files/makefile.patch
56 new file mode 100644
57 index 000000000..236da461e
58 --- /dev/null
59 +++ b/sci-biology/geneathome/files/makefile.patch
60 @@ -0,0 +1,44 @@
61 +--- a/src/Makefile
62 ++++ b/src/Makefile
63 +@@ -22,20 +22,16 @@
64 + BOINC_DIR ?= ../../..
65 + BOINC_API_DIR ?= $(BOINC_DIR)/api
66 + BOINC_LIB_DIR ?= $(BOINC_DIR)/lib
67 +-BOINC_ZIP_DIR ?= $(BOINC_DIR)/zip
68 +-BOINC_LIBS ?= $(BOINC_API_DIR)/libboinc_api.a $(BOINC_LIB_DIR)/libboinc.a
69 ++BOINC_LIBS ?= -lboinc_api -lboinc
70 +
71 + ifdef BOINC_STUB
72 + BOINC_DIR = ../boinc_stub
73 + BOINC_LIBS =
74 + endif
75 +
76 +-FREETYPE_DIR = /usr/include/freetype2
77 +-CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -I$(BOINC_ZIP_DIR) -I$(FREETYPE_DIR) -Isimd
78 +-CFLAGS += -c -O3 $(ARCH) -Wall -Wextra -pedantic -Werror $(VARIANTFLAGS) -MMD -MP
79 +-CXXFLAGS += $(CFLAGS) -std=gnu++11
80 +-LDFLAGS += $(ARCH) -L/usr/X11R6/lib -L. -static
81 +-LIBS ?= -static-libgcc -static-libstdc++ -pthread -Wl,-Bstatic -lbz2
82 ++CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -Isimd
83 ++CXXFLAGS += -std=gnu++11
84 ++LIBS ?= -pthread -lbz2
85 + CXXSOURCES = BoincFile.cpp Graph.cpp boinc_functions.cpp utility.cpp pc.cpp main.cpp
86 + CSOURCES = erf.c
87 + OBJECTS = $(CXXSOURCES:.cpp=.o) $(CSOURCES:.c=.o)
88 +@@ -44,13 +40,13 @@
89 + all: $(EXECUTABLE)
90 +
91 + $(EXECUTABLE): $(OBJECTS)
92 +- $(CXX) $(LDFLAGS) $(OBJECTS) -o $@ $(LIBS) $(BOINC_LIBS)
93 ++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) $(BOINC_LIBS)
94 +
95 + .cpp.o:
96 +- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $< -o $@
97 ++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
98 +
99 + .c.o:
100 +- $(CC) $(CPPFLAGS) $(CFLAGS) $< -o $@
101 ++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
102 +
103 + clean:
104 + rm -rf ../bin/$(EXECUTABLE) *.o *~ *.d
105
106 diff --git a/sci-biology/geneathome/geneathome-1.10.ebuild b/sci-biology/geneathome/geneathome-1.10.ebuild
107 new file mode 100644
108 index 000000000..cf16befe5
109 --- /dev/null
110 +++ b/sci-biology/geneathome/geneathome-1.10.ebuild
111 @@ -0,0 +1,78 @@
112 +# Copyright 2021 Gentoo Authors
113 +# Distributed under the terms of the GNU General Public License v2
114 +
115 +EAPI=7
116 +
117 +inherit autotools toolchain-funcs
118 +
119 +MY_PN="pc-boinc"
120 +COMMIT="3186afba409a"
121 +
122 +BOINC_VER=7.16.16
123 +BOINC_RELEASE=$(ver_cut 1-2 "${BOINC_VER}")
124 +
125 +DESCRIPTION="BOINC application for expanding Gene Regulatory Networks (GRN)"
126 +HOMEPAGE="http://gene.disi.unitn.it/test/genehome https://bitbucket.org/francesco-asnicar/pc-boinc"
127 +SRC_URI="https://github.com/BOINC/boinc/archive/client_release/${BOINC_RELEASE}/${BOINC_VER}.tar.gz -> boinc-${BOINC_VER}.tar.gz
128 + https://bitbucket.org/francesco-asnicar/${MY_PN}/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
129 +S="${WORKDIR}/boinc-client_release-${BOINC_RELEASE}-${BOINC_VER}/samples/francesco-asnicar-${MY_PN}-${COMMIT}"
130 +
131 +LICENSE="FSFAP public-domain"
132 +SLOT="0"
133 +KEYWORDS="~amd64 ~x86"
134 +
135 +DEPEND="
136 + app-arch/bzip2
137 + sci-misc/boinc
138 +"
139 +RDEPEND="${DEPEND}"
140 +BDEPEND=""
141 +
142 +PATCHES=( "${FILESDIR}"/makefile.patch )
143 +
144 +DOCS=( Readme.md )
145 +
146 +src_unpack() {
147 + default
148 + mv "${WORKDIR}/francesco-asnicar-${MY_PN}-${COMMIT}" "${S}" || die
149 +}
150 +
151 +src_prepare() {
152 + default
153 + sed 's/stdio.h/iostream/' -i src/main.cpp || die
154 + sed 's/fprintf(stderr, \(.*\))/std::cerr << \1/g' -i src/main.cpp || die
155 +
156 + cd ../.. || die
157 + eautoreconf
158 +}
159 +
160 +src_configure() {
161 + cd ../.. || die
162 + econf --enable-pkg-devel --disable-static
163 +}
164 +
165 +src_compile() {
166 + tc-export CC CXX
167 + cd src || die
168 + emake
169 +}
170 +
171 +src_test() {
172 + bash test_run.sh || die
173 + bash test_run2.sh || die
174 +}
175 +
176 +src_install() {
177 + insinto /var/lib/boinc/projects/gene.disi.unitn.it_test
178 + doins "${FILESDIR}"/app_config.xml
179 + exeinto /var/lib/boinc/projects/gene.disi.unitn.it_test
180 + newexe bin/pc "gene_pcim_v${PV}"
181 +}
182 +
183 +pkg_postinst() {
184 + elog
185 + elog "gene@home is a part of TN-Grid BOINC project."
186 + elog
187 + elog "- Master URL: https://gene.disi.unitn.it/test/"
188 + elog "- Invitation code: science@tn"
189 +}
190
191 diff --git a/sci-biology/geneathome/metadata.xml b/sci-biology/geneathome/metadata.xml
192 new file mode 100644
193 index 000000000..70e709e63
194 --- /dev/null
195 +++ b/sci-biology/geneathome/metadata.xml
196 @@ -0,0 +1,11 @@
197 +<?xml version="1.0" encoding="UTF-8"?>
198 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
199 +<pkgmetadata>
200 + <upstream>
201 + <remote-id type="bitbucket">francesco-asnicar/pc-boinc</remote-id>
202 + </upstream>
203 + <maintainer type="person">
204 + <email>cyber+gentoo@×××××.in</email>
205 + <name>Anna</name>
206 + </maintainer>
207 +</pkgmetadata>