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commit: 0b33cc8749ef3a099e2db52b2f273a602d811fbd |
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Author: Anna Vyalkova <cyber <AT> sysrq <DOT> in> |
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AuthorDate: Wed May 19 01:06:06 2021 +0000 |
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Commit: Anna Vyalkova <cyber+gentoo <AT> sysrq <DOT> in> |
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CommitDate: Wed May 19 01:06:06 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/proj/guru.git/commit/?id=0b33cc87 |
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|
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sci-biology/geneathome: initial import |
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|
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Signed-off-by: Anna Vyalkova <cyber <AT> sysrq.in> |
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|
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sci-biology/geneathome/Manifest | 2 + |
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sci-biology/geneathome/files/app_config.xml | 20 +++++++ |
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sci-biology/geneathome/files/makefile.patch | 44 +++++++++++++++ |
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sci-biology/geneathome/geneathome-1.10.ebuild | 78 +++++++++++++++++++++++++++ |
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sci-biology/geneathome/metadata.xml | 11 ++++ |
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5 files changed, 155 insertions(+) |
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|
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diff --git a/sci-biology/geneathome/Manifest b/sci-biology/geneathome/Manifest |
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new file mode 100644 |
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index 000000000..5a086b395 |
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--- /dev/null |
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+++ b/sci-biology/geneathome/Manifest |
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@@ -0,0 +1,2 @@ |
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+DIST boinc-7.16.16.tar.gz 49599131 BLAKE2B 819ab85c19a684144711f77e669b892aa73c006b81c1d7ef7adbd9d580e1e8473ae27b52dc17953ee677c70fc78ed15df936afd740e629715f30f2b81d84ea6f SHA512 dd7042e176d6506c70de7866556ae73b2f45734df92038086d5b0414751f3da08dc571c49f0c26d747d3fb2577674d3ff8cdec7d3563861eaaaa5af9c1db0a0e |
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+DIST geneathome-1.10.tar.gz 73686241 BLAKE2B 4a4e9930e3faeaf0b6d687d26adb3267af1a70096397e9e4001066a7029a854b95cd35b6779a0e6bcf6c9cb3ad662b5f9e6adf4ab9d608ed2d73c65d3dadc10b SHA512 c8c1bb65f0021d9c9d9f14375212c458694dbb21abbfa90f6b8fb958bc6d86a522bbe13846b5930f6df0a4e755256f2016c5edd4447ae147cb1381eccce06b9e |
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|
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diff --git a/sci-biology/geneathome/files/app_config.xml b/sci-biology/geneathome/files/app_config.xml |
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new file mode 100644 |
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index 000000000..43b80156b |
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--- /dev/null |
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+++ b/sci-biology/geneathome/files/app_config.xml |
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@@ -0,0 +1,20 @@ |
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+<app_info> |
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+<app> |
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+ <name>gene_pcim</name> |
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+ <user_friendly_name>gene@home PC-IM</user_friendly_name> |
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+</app> |
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+ |
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+<file_info> |
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+ <name>gene_pcim_v1.10</name> |
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+ <executable/> |
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+</file_info> |
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+ |
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+<app_version> |
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+ <app_name>gene_pcim</app_name> |
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+ <version_num>110</version_num> |
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+ <file_ref> |
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+ <file_name>gene_pcim_v1.10</file_name> |
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+ <main_program/> |
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+ </file_ref> |
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+</app_version> |
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+</app_info> |
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|
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diff --git a/sci-biology/geneathome/files/makefile.patch b/sci-biology/geneathome/files/makefile.patch |
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new file mode 100644 |
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index 000000000..236da461e |
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--- /dev/null |
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+++ b/sci-biology/geneathome/files/makefile.patch |
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@@ -0,0 +1,44 @@ |
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+--- a/src/Makefile |
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++++ b/src/Makefile |
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+@@ -22,20 +22,16 @@ |
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+ BOINC_DIR ?= ../../.. |
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+ BOINC_API_DIR ?= $(BOINC_DIR)/api |
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+ BOINC_LIB_DIR ?= $(BOINC_DIR)/lib |
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+-BOINC_ZIP_DIR ?= $(BOINC_DIR)/zip |
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+-BOINC_LIBS ?= $(BOINC_API_DIR)/libboinc_api.a $(BOINC_LIB_DIR)/libboinc.a |
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++BOINC_LIBS ?= -lboinc_api -lboinc |
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+ |
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+ ifdef BOINC_STUB |
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+ BOINC_DIR = ../boinc_stub |
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+ BOINC_LIBS = |
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+ endif |
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+ |
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+-FREETYPE_DIR = /usr/include/freetype2 |
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+-CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -I$(BOINC_ZIP_DIR) -I$(FREETYPE_DIR) -Isimd |
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+-CFLAGS += -c -O3 $(ARCH) -Wall -Wextra -pedantic -Werror $(VARIANTFLAGS) -MMD -MP |
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+-CXXFLAGS += $(CFLAGS) -std=gnu++11 |
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+-LDFLAGS += $(ARCH) -L/usr/X11R6/lib -L. -static |
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+-LIBS ?= -static-libgcc -static-libstdc++ -pthread -Wl,-Bstatic -lbz2 |
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++CPPFLAGS += -I$(BOINC_DIR) -I$(BOINC_LIB_DIR) -I$(BOINC_API_DIR) -Isimd |
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++CXXFLAGS += -std=gnu++11 |
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++LIBS ?= -pthread -lbz2 |
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+ CXXSOURCES = BoincFile.cpp Graph.cpp boinc_functions.cpp utility.cpp pc.cpp main.cpp |
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+ CSOURCES = erf.c |
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+ OBJECTS = $(CXXSOURCES:.cpp=.o) $(CSOURCES:.c=.o) |
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+@@ -44,13 +40,13 @@ |
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+ all: $(EXECUTABLE) |
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+ |
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+ $(EXECUTABLE): $(OBJECTS) |
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+- $(CXX) $(LDFLAGS) $(OBJECTS) -o $@ $(LIBS) $(BOINC_LIBS) |
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++ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) $(BOINC_LIBS) |
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+ |
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+ .cpp.o: |
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+- $(CXX) $(CPPFLAGS) $(CXXFLAGS) $< -o $@ |
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++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@ |
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+ |
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+ .c.o: |
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+- $(CC) $(CPPFLAGS) $(CFLAGS) $< -o $@ |
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++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@ |
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+ |
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+ clean: |
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+ rm -rf ../bin/$(EXECUTABLE) *.o *~ *.d |
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|
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diff --git a/sci-biology/geneathome/geneathome-1.10.ebuild b/sci-biology/geneathome/geneathome-1.10.ebuild |
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new file mode 100644 |
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index 000000000..cf16befe5 |
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--- /dev/null |
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+++ b/sci-biology/geneathome/geneathome-1.10.ebuild |
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@@ -0,0 +1,78 @@ |
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+# Copyright 2021 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+ |
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+inherit autotools toolchain-funcs |
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+ |
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+MY_PN="pc-boinc" |
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+COMMIT="3186afba409a" |
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+ |
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+BOINC_VER=7.16.16 |
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+BOINC_RELEASE=$(ver_cut 1-2 "${BOINC_VER}") |
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+ |
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+DESCRIPTION="BOINC application for expanding Gene Regulatory Networks (GRN)" |
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+HOMEPAGE="http://gene.disi.unitn.it/test/genehome https://bitbucket.org/francesco-asnicar/pc-boinc" |
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+SRC_URI="https://github.com/BOINC/boinc/archive/client_release/${BOINC_RELEASE}/${BOINC_VER}.tar.gz -> boinc-${BOINC_VER}.tar.gz |
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+ https://bitbucket.org/francesco-asnicar/${MY_PN}/get/${COMMIT}.tar.gz -> ${P}.tar.gz" |
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+S="${WORKDIR}/boinc-client_release-${BOINC_RELEASE}-${BOINC_VER}/samples/francesco-asnicar-${MY_PN}-${COMMIT}" |
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+ |
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+LICENSE="FSFAP public-domain" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+ |
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+DEPEND=" |
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+ app-arch/bzip2 |
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+ sci-misc/boinc |
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+" |
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+RDEPEND="${DEPEND}" |
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+BDEPEND="" |
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+ |
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+PATCHES=( "${FILESDIR}"/makefile.patch ) |
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+ |
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+DOCS=( Readme.md ) |
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+ |
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+src_unpack() { |
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+ default |
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+ mv "${WORKDIR}/francesco-asnicar-${MY_PN}-${COMMIT}" "${S}" || die |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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+ sed 's/stdio.h/iostream/' -i src/main.cpp || die |
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+ sed 's/fprintf(stderr, \(.*\))/std::cerr << \1/g' -i src/main.cpp || die |
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+ |
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+ cd ../.. || die |
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+ eautoreconf |
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+} |
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+ |
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+src_configure() { |
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+ cd ../.. || die |
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+ econf --enable-pkg-devel --disable-static |
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+} |
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+ |
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+src_compile() { |
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+ tc-export CC CXX |
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+ cd src || die |
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+ emake |
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+} |
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+ |
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+src_test() { |
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+ bash test_run.sh || die |
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+ bash test_run2.sh || die |
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+} |
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+ |
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+src_install() { |
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+ insinto /var/lib/boinc/projects/gene.disi.unitn.it_test |
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+ doins "${FILESDIR}"/app_config.xml |
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+ exeinto /var/lib/boinc/projects/gene.disi.unitn.it_test |
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+ newexe bin/pc "gene_pcim_v${PV}" |
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+} |
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+ |
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+pkg_postinst() { |
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+ elog |
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+ elog "gene@home is a part of TN-Grid BOINC project." |
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+ elog |
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+ elog "- Master URL: https://gene.disi.unitn.it/test/" |
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+ elog "- Invitation code: science@tn" |
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+} |
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|
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diff --git a/sci-biology/geneathome/metadata.xml b/sci-biology/geneathome/metadata.xml |
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new file mode 100644 |
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index 000000000..70e709e63 |
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--- /dev/null |
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+++ b/sci-biology/geneathome/metadata.xml |
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@@ -0,0 +1,11 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <upstream> |
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+ <remote-id type="bitbucket">francesco-asnicar/pc-boinc</remote-id> |
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+ </upstream> |
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+ <maintainer type="person"> |
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+ <email>cyber+gentoo@×××××.in</email> |
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+ <name>Anna</name> |
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+ </maintainer> |
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+</pkgmetadata> |