sci-biology/geneathome: initial import

Signed-off-by: Anna Vyalkova <cyber@sysrq.in>

5 files changed, 155 insertions, 0 deletions

diff --git a/sci-biology/geneathome/Manifest b/sci-biology/geneathome/Manifest
new file mode 100644
index 000000000..5a086b395
--- /dev/null
+++ b/sci-biology/geneathome/Manifest
@@ -0,0 +1,2 @@
+DIST boinc-7.16.16.tar.gz 49599131 BLAKE2B 819ab85c19a684144711f77e669b892aa73c006b81c1d7ef7adbd9d580e1e8473ae27b52dc17953ee677c70fc78ed15df936afd740e629715f30f2b81d84ea6f SHA512 dd7042e176d6506c70de7866556ae73b2f45734df92038086d5b0414751f3da08dc571c49f0c26d747d3fb2577674d3ff8cdec7d3563861eaaaa5af9c1db0a0e
+DIST geneathome-1.10.tar.gz 73686241 BLAKE2B 4a4e9930e3faeaf0b6d687d26adb3267af1a70096397e9e4001066a7029a854b95cd35b6779a0e6bcf6c9cb3ad662b5f9e6adf4ab9d608ed2d73c65d3dadc10b SHA512 c8c1bb65f0021d9c9d9f14375212c458694dbb21abbfa90f6b8fb958bc6d86a522bbe13846b5930f6df0a4e755256f2016c5edd4447ae147cb1381eccce06b9e
diff --git a/sci-biology/geneathome/files/app_config.xml b/sci-biology/geneathome/files/app_config.xml
new file mode 100644
index 000000000..43b80156b
--- /dev/null
+++ b/sci-biology/geneathome/files/app_config.xml
@@ -0,0 +1,20 @@
+<app_info>
+<app>
+	<name>gene_pcim</name>
+	<user_friendly_name>gene@home PC-IM</user_friendly_name>
+</app>
+
+<file_info>
+	<name>gene_pcim_v1.10</name>
+	<executable/>
+</file_info>
+
+<app_version>
+	<app_name>gene_pcim</app_name>
+	<version_num>110</version_num>
+	<file_ref>
+		<file_name>gene_pcim_v1.10</file_name>
+		<main_program/>
+	</file_ref>
+</app_version>
+</app_info>
diff --git a/sci-biology/geneathome/files/makefile.patch b/sci-biology/geneathome/files/makefile.patch
new file mode 100644
index 000000000..236da461e
--- /dev/null
+++ b/sci-biology/geneathome/files/makefile.patch
@@ -0,0 +1,44 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -22,20 +22,16 @@
+ BOINC_DIR ?= ../../..
+ BOINC_API_DIR ?= $(BOINC_DIR)/api
+ BOINC_LIB_DIR ?= $(BOINC_DIR)/lib
+-BOINC_ZIP_DIR ?= $(BOINC_DIR)/zip
+-BOINC_LIBS ?= $(BOINC_API_DIR)/libboinc_api.a $(BOINC_LIB_DIR)/libboinc.a
++BOINC_LIBS ?= -lboinc_api -lboinc
+ 
+ ifdef BOINC_STUB
+ BOINC_DIR = ../boinc_stub
+ BOINC_LIBS =
+ endif
+ 
+-FREETYPE_DIR = /usr/include/freetype2
+-CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -I$(BOINC_ZIP_DIR) -I$(FREETYPE_DIR) -Isimd
+-CFLAGS += -c -O3 $(ARCH) -Wall -Wextra -pedantic -Werror $(VARIANTFLAGS)  -MMD -MP
+-CXXFLAGS += $(CFLAGS) -std=gnu++11
+-LDFLAGS += $(ARCH) -L/usr/X11R6/lib -L. -static
+-LIBS ?= -static-libgcc -static-libstdc++ -pthread -Wl,-Bstatic -lbz2
++CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -Isimd
++CXXFLAGS += -std=gnu++11
++LIBS ?= -pthread -lbz2
+ CXXSOURCES = BoincFile.cpp Graph.cpp boinc_functions.cpp utility.cpp pc.cpp main.cpp
+ CSOURCES = erf.c
+ OBJECTS = $(CXXSOURCES:.cpp=.o) $(CSOURCES:.c=.o)
+@@ -44,13 +40,13 @@
+ all: $(EXECUTABLE)
+ 
+ $(EXECUTABLE): $(OBJECTS)
+-	$(CXX) $(LDFLAGS) $(OBJECTS) -o $@ $(LIBS) $(BOINC_LIBS)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) $(BOINC_LIBS)
+ 
+ .cpp.o:
+-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $< -o $@
++	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
+ 
+ .c.o:
+-	$(CC) $(CPPFLAGS) $(CFLAGS) $< -o $@
++	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
+ 
+ clean:
+ 	rm -rf ../bin/$(EXECUTABLE) *.o *~ *.d
diff --git a/sci-biology/geneathome/geneathome-1.10.ebuild b/sci-biology/geneathome/geneathome-1.10.ebuild
new file mode 100644
index 000000000..cf16befe5
--- /dev/null
+++ b/sci-biology/geneathome/geneathome-1.10.ebuild
@@ -0,0 +1,78 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+MY_PN="pc-boinc"
+COMMIT="3186afba409a"
+
+BOINC_VER=7.16.16
+BOINC_RELEASE=$(ver_cut 1-2 "${BOINC_VER}")
+
+DESCRIPTION="BOINC application for expanding Gene Regulatory Networks (GRN)"
+HOMEPAGE="http://gene.disi.unitn.it/test/genehome https://bitbucket.org/francesco-asnicar/pc-boinc"
+SRC_URI="https://github.com/BOINC/boinc/archive/client_release/${BOINC_RELEASE}/${BOINC_VER}.tar.gz -> boinc-${BOINC_VER}.tar.gz
+	https://bitbucket.org/francesco-asnicar/${MY_PN}/get/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/boinc-client_release-${BOINC_RELEASE}-${BOINC_VER}/samples/francesco-asnicar-${MY_PN}-${COMMIT}"
+
+LICENSE="FSFAP public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+	app-arch/bzip2
+	sci-misc/boinc
+"
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+PATCHES=( "${FILESDIR}"/makefile.patch )
+
+DOCS=( Readme.md )
+
+src_unpack() {
+	default
+	mv "${WORKDIR}/francesco-asnicar-${MY_PN}-${COMMIT}" "${S}" || die
+}
+
+src_prepare() {
+	default
+	sed 's/stdio.h/iostream/' -i src/main.cpp || die
+	sed 's/fprintf(stderr, \(.*\))/std::cerr << \1/g' -i src/main.cpp || die
+
+	cd ../.. || die
+	eautoreconf
+}
+
+src_configure() {
+	cd ../.. || die
+	econf --enable-pkg-devel --disable-static
+}
+
+src_compile() {
+	tc-export CC CXX
+	cd src || die
+	emake
+}
+
+src_test() {
+	bash test_run.sh || die
+	bash test_run2.sh || die
+}
+
+src_install() {
+	insinto /var/lib/boinc/projects/gene.disi.unitn.it_test
+	doins "${FILESDIR}"/app_config.xml
+	exeinto /var/lib/boinc/projects/gene.disi.unitn.it_test
+	newexe bin/pc "gene_pcim_v${PV}"
+}
+
+pkg_postinst() {
+	elog
+	elog "gene@home is a part of TN-Grid BOINC project."
+	elog
+	elog "- Master URL: https://gene.disi.unitn.it/test/"
+	elog "- Invitation code: science@tn"
+}
diff --git a/sci-biology/geneathome/metadata.xml b/sci-biology/geneathome/metadata.xml
new file mode 100644
index 000000000..70e709e63
--- /dev/null
+++ b/sci-biology/geneathome/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<upstream>
+		<remote-id type="bitbucket">francesco-asnicar/pc-boinc</remote-id>
+	</upstream>
+	<maintainer type="person">
+		<email>cyber+gentoo@sysrq.in</email>
+		<name>Anna</name>
+	</maintainer>
+</pkgmetadata>