reinit the tree, so we can have metadata

5 files changed, 322 insertions, 0 deletions

diff --git a/sci-biology/blossoc/Manifest b/sci-biology/blossoc/Manifest
new file mode 100644
index 000000000000..0a75c9164e33
--- /dev/null
+++ b/sci-biology/blossoc/Manifest
@@ -0,0 +1,7 @@
+AUX blossoc-1.4.0-fix-build-system.patch 8380 SHA256 ea66141979346a032ede2fd9653a71e59ce580ff9a89f4b022f2aff01b35315a SHA512 e1e97db5446916fd3ea7ca84baddde4771f6ee0081e17bd28e473a85565c1f0d1aa5e4385ee77a473f67eb5dd36eff7849dd334e31e4a4e1fb47737e3597e091 WHIRLPOOL ec2d035582d870204e6ee0dd201f05cb76fbc8d683da44c1c6787bd6eb762469038a76c8d6311579ed7af878bfa61577cbb737e0bd16f1024f276498ed7707b7
+AUX blossoc-1.4.0-gcc43.patch 303 SHA256 d8e558d1407d7e0f9ade2ff32fa84ee924a4412df55a9f270bb7a3f96d6e821b SHA512 600890d9e40f56923c84e181957abfb2e75b66992b3f7b406f15a6cdb779527868e6b37c573e9b22e81964ff0600080b73ec967df60ed8d9fcfc84c2e6810093 WHIRLPOOL badc2e444303838e211665472c9e13f1760fadb4107d807ccc270923eb35a33d64518024ffacc83c26e4dbc09e319011a47f03f41f4a41a39b9fae0c49c6f217
+DIST blossoc-1.4.0.tar.gz 194885 SHA256 b23f51349f72f31263b8aca162c7590a5f52b72fd5e0d91b4a2591098ff5bdbe SHA512 fd47c85df5f1f97527e1abb1e56b05c02fa44c1c110abc222d895b2370324a26970446084e62adf02ce0c7dc332635d40dd1505d423571b424865425f6b2a327 WHIRLPOOL b826dfda205b93613519f84b17e3b1f9b28274b7badd6207f5fefa5117633cda4a4077394053d9add11f771e859f1d3d060e97d5e8d95010ba571e26abae5313
+EBUILD blossoc-1.4.0-r1.ebuild 726 SHA256 3b056fd013939020e72fcb6a7663ea63bb7d343606732733da945a2e2dc3cb13 SHA512 f345c811c9dd49b716ec91a5cb3460a763cc125fe93a5a45a29245a08544455dd9686264e69333c54c5cc736b2b5d0cd76bc7e9b3cd279c5264a83726d81067b WHIRLPOOL 19af94650fa624360afa2cba378de3d571ffd90eccf1eb96dc8156ed8f6714022be64487090e69fe14f47ebadcc55f41e565d3c934fc1b2deb5de5d440c05d05
+MISC ChangeLog 2464 SHA256 36beabb2c743627a2a722b8afef186f64142e7d7163ea2f6634fb5f34d22d920 SHA512 dc0d98d68f5ce9170b94a3676b9ed4bfc90e1c673d35276da5628bffc48d87b2383d786e499d13df2a7c8a6f9d126d9dd7351d38066f383ec3a08513e519e4f7 WHIRLPOOL a20ee188de84a159bd94c6daa93c998e6f12906ae6b8614b564d9094cfaa5b384e8c223fe91347693e4feb2b14da2b87a45bb57bbf028b06df304338addd7705
+MISC ChangeLog-2015 872 SHA256 7be6da7e6bc5838a5c738d0ea637f8d3fb3ab6e11a023b5ef02991c23d71605b SHA512 75bd413cdca1ddbdf5c645653d5fb1684aa0ff1252a0b9baf9aaba391e6831e731ab6566fb5b81c52a7bb84e01db9a84f08d21f599997dd52bc8802d21d72865 WHIRLPOOL 49aba78c0b6e6e4b7117256d5306d8657ba657f68438f8c72e60d7679733609f417a7ebaaaf0df2a3ec988bac436a3930c90d4f1d10da724d26546fd3fbb1924
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
new file mode 100644
index 000000000000..9fd1189e025a
--- /dev/null
+++ b/sci-biology/blossoc/blossoc-1.4.0-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="A linkage disequilibrium association mapping tool"
+HOMEPAGE="http://www.daimi.au.dk/~mailund/Blossoc/"
+SRC_URI="http://www.daimi.au.dk/~mailund/Blossoc/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-libs/gsl:=
+	dev-libs/boost:=
+	sci-biology/snpfile"
+DEPEND="
+	${RDEPEND}
+	>=sys-devel/autoconf-archive-2016.09.16
+	virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.4.0-gcc43.patch
+	"${FILESDIR}"/${PN}-1.4.0-fix-build-system.patch
+)
+
+src_prepare() {
+	default
+	mv configure.{in,ac} || die
+	rm m4/ax_boost.m4 || die
+	eautoreconf
+}
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
new file mode 100644
index 000000000000..21234cc3cfb3
--- /dev/null
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-fix-build-system.patch
@@ -0,0 +1,256 @@
+* Modernise Autoconf code
+* Use pkg-config for finding GSL
+* Use latest archvie macros to find Boost
+* Compile tests only when running make check
+
+--- a/configure.in
++++ b/configure.in
+@@ -1,6 +1,6 @@
+ AC_INIT(blossoc, 1.4.0, mailund@birc.au.dk)
+ AM_INIT_AUTOMAKE
+-AM_CONFIG_HEADER(config.hh)
++AC_CONFIG_HEADERS([config.hh])
+ 
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+@@ -12,74 +12,16 @@
+ fi
+ AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix])
+ 
+-AC_CHECK_LIB(m, sin, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-Didn't find the math library (-lm) -- I won't even guess about what is
+-wrong on this machine...
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AX_BOOST([1.33.1],,
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The Boost library was not found on this system.  We use this library
+-extensively, and cannot proceed without it.  You can obtain it from
+-<http://www.boost.org>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-
+-AC_CHECK_LIB(gslcblas, cblas_dsdot, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The GNU Scientific Library (GSL) was not found.  This library is
+-needed for some of the numerical calculations used for scoring the
+-significance of local genealogies and can be obtained at
+-<http://www.gnu.org/software/gsl/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AC_CHECK_LIB(gsl, gsl_cdf_chisq_Q, dnl FOUND, DO NOTHING
+-, dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The GNU Scientific Library (GSL) was not found.  This library is
+-needed for some of the numerical calculations used for scoring the
+-significance of local genealogies and can be obtained at
+-<http://www.gnu.org/software/gsl/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
+-AC_CHECK_LIB(snpfile, main, dnl main isn't there, but this avoids namespaces
+-dnl FOUND
+-,
+-dnl NOT FOUND
+-AC_ERROR([[
+-************************************************************************
+-************************************************************************
+-The SNPFile library was not found.  This library is needed for data
+-representation and can be obtained at
+-<http://www.birc.au.dk/~mailund/SNPFile/>.
+-************************************************************************
+-************************************************************************
+-]])
+-)
+-
++AC_SEARCH_LIBS([sin], [m], [], [
++	AC_MSG_ERROR([unable to find the sin() function])
++])
++
++PKG_CHECK_MODULES([GSL], [gsl])
++
++AX_BOOST_BASE([1.33.1])
++AX_BOOST_PROGRAM_OPTIONS
++AX_BOOST_SERIALIZATION
++AX_BOOST_SIGNALS
+ 
+ AC_OUTPUT([
+ 	Makefile
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -3,9 +3,6 @@
+ AM_CXXFLAGS += -Wall
+ AM_CXXFLAGS += $(BOOST_CPPFLAGS)
+ 
+-# for testing
+-AM_CXXFLAGS += -g -O0 #-lefence
+-
+ # for coverage testing
+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -g -fprofile-arcs -ftest-coverage
+ 
+@@ -15,11 +12,11 @@
+ # for production
+ #AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG
+ 
+-noinst_PROGRAMS = 
++check_PROGRAMS =
++noinst_PROGRAMS =
+ TESTS = 
+ EXTRA_DIST =
+ 
+-TESTS += first_test.sh
+ EXTRA_DIST += first_test.sh
+ 
+ man_MANS = blossoc.1 snpfile_blossoc.1 blossoc_regions.1 blossoc_trees.1
+@@ -37,20 +34,20 @@
+ noinst_PROGRAMS     += snpfile_iblossoc #ditto
+ noinst_PROGRAMS     += fast_snpfile_iblossoc
+ 
+-noinst_PROGRAMS += matrix_test
+-TESTS +=           matrix_test
+-noinst_PROGRAMS += incompatibility_test tree_test tree_builder_test
+-TESTS +=           incompatibility_test tree_test tree_builder_test
++check_PROGRAMS += matrix_test
++TESTS +=          matrix_test
++check_PROGRAMS += incompatibility_test tree_test tree_builder_test
++TESTS +=          incompatibility_test tree_test tree_builder_test
+ EXTRA_DIST += testdata/CF/cf-positions.txt
+ EXTRA_DIST += testdata/CF/cf-haplotypes.txt
+ EXTRA_DIST += testdata/interaction/positions.txt
+ EXTRA_DIST += testdata/interaction/haplotypes.txt
+-noinst_PROGRAMS += score_test io_test 
+-TESTS +=           score_test io_test 
+-noinst_PROGRAMS += incompatible_regress_test
+-TESTS +=           incompatible_regress_test
+-noinst_PROGRAMS += genotype_score_test
+-TESTS +=           genotype_score_test.sh
++check_PROGRAMS += score_test io_test 
++TESTS +=          score_test io_test 
++check_PROGRAMS += incompatible_regress_test
++TESTS +=          incompatible_regress_test
++check_PROGRAMS += genotype_score_test
++TESTS +=          genotype_score_test.sh
+ EXTRA_DIST += genotype_score_test.sh
+ EXTRA_DIST += genotype_score_test.expected
+ TESTS +=           interactions_regression_test.sh
+@@ -120,6 +117,7 @@
+ 
+ 
+ blossoc_regions_LDADD  =
++blossoc_regions_LDADD += -lsnpfile
+ blossoc_regions_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_regions_SOURCES  =
+ blossoc_regions_SOURCES += incompatibility.hh incompatibility.cc
+@@ -129,6 +127,7 @@
+ blossoc_regions_SOURCES += regions.cc
+ 
+ blossoc_trees_LDADD  =
++blossoc_trees_LDADD += -lsnpfile
+ blossoc_trees_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_trees_SOURCES  =
+ blossoc_trees_SOURCES += matrix_utils.hh matrix_utils.cc 
+@@ -142,6 +141,8 @@
+ 
+ 
+ blossoc_LDADD  =
++blossoc_LDADD += -lsnpfile
++blossoc_LDADD += $(GSL_LIBS)
+ blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ blossoc_SOURCES  =
+ blossoc_SOURCES += tree.hh tree.cc
+@@ -158,6 +159,8 @@
+ blossoc_SOURCES += blossoc.cc
+ 
+ snpfile_blossoc_LDADD  =
++snpfile_blossoc_LDADD += -lsnpfile
++snpfile_blossoc_LDADD += $(GSL_LIBS)
+ snpfile_blossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ snpfile_blossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ snpfile_blossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -176,6 +179,8 @@
+ snpfile_blossoc_SOURCES += snpfile_blossoc.cc
+ 
+ iblossoc_LDADD  =
++iblossoc_LDADD += -lsnpfile
++iblossoc_LDADD += $(GSL_LIBS)
+ iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ iblossoc_SOURCES  =
+ iblossoc_SOURCES += tree.hh tree.cc
+@@ -191,6 +196,8 @@
+ iblossoc_SOURCES += interactions.cc
+ 
+ low_mem_iblossoc_LDADD  =
++low_mem_iblossoc_LDADD += -lsnpfile
++low_mem_iblossoc_LDADD += $(GSL_LIBS)
+ low_mem_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ low_mem_iblossoc_SOURCES  =
+ low_mem_iblossoc_SOURCES += tree.hh tree.cc
+@@ -206,6 +213,8 @@
+ low_mem_iblossoc_SOURCES += low_mem_interactions.cc
+ 
+ snpfile_iblossoc_LDADD  =
++snpfile_iblossoc_LDADD += -lsnpfile
++snpfile_iblossoc_LDADD += $(GSL_LIBS)
+ snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -223,6 +232,8 @@
+ snpfile_iblossoc_SOURCES += snpfile_interactions.cc
+ 
+ fast_snpfile_iblossoc_LDADD  =
++fast_snpfile_iblossoc_LDADD += -lsnpfile
++fast_snpfile_iblossoc_LDADD += $(GSL_LIBS)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_SERIALIZATION_LIB)
+ fast_snpfile_iblossoc_LDADD += $(BOOST_SIGNALS_LIB)
+@@ -239,6 +250,28 @@
+ fast_snpfile_iblossoc_SOURCES += io.hh io.cc
+ fast_snpfile_iblossoc_SOURCES += fast_snpfile_interactions.cc
+ 
++matrix_test_LDADD  =
++matrix_test_LDADD += -lsnpfile
++
++incompatibility_test_LDADD  =
++incompatibility_test_LDADD += -lsnpfile
++
++tree_builder_test_LDADD  =
++tree_builder_test_LDADD += -lsnpfile
++
++score_test_LDADD  =
++score_test_LDADD += -lsnpfile
++score_test_LDADD += $(GSL_LIBS)
++
++io_test_LDADD  =
++io_test_LDADD += -lsnpfile
++
++incompatible_regress_test_LDADD  =
++incompatible_regress_test_LDADD += -lsnpfile
++
++genotype_score_test_LDADD  =
++genotype_score_test_LDADD += -lsnpfile
++genotype_score_test_LDADD += $(GSL_LIBS)
+ 
+ 
+ # include GUI in source distributions...
diff --git a/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
new file mode 100644
index 000000000000..64b5fe46e30e
--- /dev/null
+++ b/sci-biology/blossoc/files/blossoc-1.4.0-gcc43.patch
@@ -0,0 +1,15 @@
+Fixes build with >=GCC-4.3
+
+http://bugs.gentoo.org/show_bug.cgi?id=292949
+
+Patch written by Sebastian Luther <SebastianLuther@gmx.de>
+--- a/pph.cc
++++ b/pph.cc
+@@ -23,6 +23,7 @@
+  */
+ 
+ #include "pph.hh"
++#include <cstdio>
+ #include <cmath>
+ #include <snpfile/matrix.hh>
+ using namespace BiRC::SNPFile;
diff --git a/sci-biology/blossoc/metadata.xml b/sci-biology/blossoc/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/blossoc/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>