From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/snpfile/Manifest | 9 + .../snpfile/files/snpfile-2.0.1-ax-boost.patch | 35 ++ .../snpfile/files/snpfile-2.0.1-gcc44.patch | 12 + .../snpfile/files/snpfile-2.0.1-gentoo.diff | 533 +++++++++++++++++++++ sci-biology/snpfile/files/snpfile-2.0.1-gold.patch | 23 + sci-biology/snpfile/metadata.xml | 8 + sci-biology/snpfile/snpfile-2.0.1-r2.ebuild | 46 ++ 7 files changed, 666 insertions(+) create mode 100644 sci-biology/snpfile/Manifest create mode 100644 sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch create mode 100644 sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch create mode 100644 sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff create mode 100644 sci-biology/snpfile/files/snpfile-2.0.1-gold.patch create mode 100644 sci-biology/snpfile/metadata.xml create mode 100644 sci-biology/snpfile/snpfile-2.0.1-r2.ebuild (limited to 'sci-biology/snpfile') diff --git a/sci-biology/snpfile/Manifest b/sci-biology/snpfile/Manifest new file mode 100644 index 000000000000..d90be00d3b92 --- /dev/null +++ b/sci-biology/snpfile/Manifest @@ -0,0 +1,9 @@ +AUX snpfile-2.0.1-ax-boost.patch 973 SHA256 a698df5bd1bfe04f40cdec8275fe3fecfced9c0e8cb43939e9b70cf3fd25cb5a SHA512 cb517e30c06620de9d007261d238325daf48709ccd875d90c0cc99049dfd0ce80a506a3e9a97c786ac8329b1f1463a810407927cf17c1a25689b03f413417b94 WHIRLPOOL e91815cd15321f0bbb62d9e73a9ea3ed80027b284a7a81d42c3c49c249f0dc6e8d23419f6606d0e51083fbf53f200168f60c26d6bf09a59d3bff7a34397783e3 +AUX snpfile-2.0.1-gcc44.patch 387 SHA256 349c6594759f16da2602415ff217c37bb677e2508437497b508c91ab4668956a SHA512 ac66850cae2bbbad9e1a989772490eb23ea3958c233e0fe32b20ffb3d7b5f547ff9d045974170c3302e8ca6bbbe5a2055acad24bb80cc6a3c527c3164e3f0e84 WHIRLPOOL f72f1321fce7941981780246d8837d260097eaf71ad1f352ae2f7407971a6625f2f9fc319904bb95ceba190d9e51b63212901798f8bcd31114e7724eee6adc00 +AUX snpfile-2.0.1-gentoo.diff 20224 SHA256 b3275446db38b35999aa25bc2aeedec63b206baa8e4d339d256b7d25e425d1df SHA512 8628aa298b38376e439739c813ec87c80eb7c7f7874335e8f812eee05fab205ae900a00ec819021699fe835c2e9d38f880e9b391ccc4bfb46a8b91f028ed84ad WHIRLPOOL e96fda8d8f54ed912f48bfd539fa04a41c436f6e4b097f96baa6b1864dac2b55bc67a2ba309466c25b3bbc995d38517b7ee0a497107b9ea69cf8d2a2d982750e +AUX snpfile-2.0.1-gold.patch 1066 SHA256 e9c256f07aacf233a5bf159fd25f536f91b650b425f9f8e39f83ac03741600e8 SHA512 81f2e5e91890e52cf40553ea70b12cdb09e5b8335303d72f6943e0058b62eb061eea4e52595c267de81af219f7b863025fb2aa7364d976101628b1f65ba27075 WHIRLPOOL 52465222846642807e2a721d8528dedb9cd5fdf3da1db8b793ed94d6ac3ef1fcab61621b4fceb0ee6eb5b6f99d89ac8bcaf584404bb1a8b4d064084e0535a69f +DIST snpfile-2.0.1.tar.gz 171854 SHA256 71569e0dcd426447d1a5d215fb47615074a4c8d935cf70ef63c5f47a411b0b76 SHA512 e217e8b600d3ba7e2a8a0724d867bd9760572398f2e4e58625c1f74b0db9aa913db266da51fcfc05b90f3faf9eb6fbeb7bd988f105de013b51c24caa37c678c6 WHIRLPOOL c47391cde1a2fa8a93a1ab6ae0ee7e32519833fe08fd87ddc0ef0872e6bc9269ad0dc609b7c09a52248793dd0b31dcdc88a0528e966c4fa5845f4ae8c943ab9c +EBUILD snpfile-2.0.1-r2.ebuild 886 SHA256 f8d6e6258b0174b926aa725f82d55aa7fb01a4b61e32f2eb5d2a4a1c9a32f0bc SHA512 7946475e80f92a1c76a4e92500cfad3f6eb4e0463014e07eb517f6a4ef0fb3ebff7143d18d22c887d970f186cc7a0847788d8b55e5b297d04820a9dfdb3475fa WHIRLPOOL a1e0f738ad79878d0fee33d6cd65a3a2ae86e011b777e56ab18e64c718970888284aecba4ffae382c2452e2b7da21bb2911aab473e3cb982d550898f61d0f330 +MISC ChangeLog 2593 SHA256 d47b1963a522cb0aa61fcac9c99bc19048532c6529acd17c35ec129bae26b3c9 SHA512 cdf29488256a34f777645873d76cc937d09358d9ed7595bf1ea88cea9d76d7afd0c8b5807bd2ffa45743b9cbeec3387b22f78c1c4615b6d7ffa427168ee8ff81 WHIRLPOOL de7ff1cae0892016453fc5585a026315e015cf7a77256e37f729f4ea13b8ffb306c3da397f9aeb265c02a72e4cb9f14983feb37ec696c0557f913aeb054408e7 +MISC ChangeLog-2015 1830 SHA256 4c163b37a8e5d54243edb64561dba7a7053b78a78c8292ce659abf802628daf3 SHA512 f1f9fd9c8afbf372df12122953fceae78c14e2835843ad48587cb2aff073cd1bdad5bc70e2b9ca4a74d4f6e63ae6acaf92fff815d411c25fef56596b3841df2e WHIRLPOOL 07f7460167f61aabf397d418c194ad02f0e00f23240a4e28b39aa3aec01524a9664fb78d3c6e90f76b2def9cfe12a639fe9460dee115be34972c156d845b9b90 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch new file mode 100644 index 000000000000..f77b476f990d --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-ax-boost.patch @@ -0,0 +1,35 @@ +Modernise autoconf code to use modern archive macros. + +--- a/configure.in ++++ b/configure.in +@@ -1,7 +1,7 @@ + AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) + AM_INIT_AUTOMAKE + AC_CONFIG_MACRO_DIR([m4]) +-AM_CONFIG_HEADER(config.hh) ++AC_CONFIG_HEADERS([config.hh]) + + LT_INIT + AC_PROG_CXX +@@ -14,18 +14,9 @@ + fi + AC_DEFINE_UNQUOTED(PREFIX, "$thePREFIX", [Installation prefix]) + +-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 +-. +-************************************************************************ +-************************************************************************ +-]]) +-) +- ++AX_BOOST_BASE([1.33.1]) ++AX_BOOST_PROGRAM_OPTIONS ++AX_BOOST_SIGNALS + + AC_OUTPUT([ + Makefile diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch new file mode 100644 index 000000000000..2b79c2492ede --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gcc44.patch @@ -0,0 +1,12 @@ +diff -ur snpfile-2.0.1.orig/input_archive.hh snpfile-2.0.1/input_archive.hh +--- snpfile-2.0.1.orig/input_archive.hh 2008-05-03 17:25:44.000000000 +0300 ++++ snpfile-2.0.1/input_archive.hh 2009-07-26 21:26:10.000000000 +0300 +@@ -26,6 +26,8 @@ + #ifndef INPUT_ARCHIVE_HH_INCLUDED + #define INPUT_ARCHIVE_HH_INCLUDED + ++#include ++ + #include + + #include "archive_common.hh" diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff new file mode 100644 index 000000000000..b2a8a6b630ce --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gentoo.diff @@ -0,0 +1,533 @@ +Fixing as-needed issues, provide shared libs + +https://bugs.gentoo.org/show_bug.cgi?id=294971 + +--- a/Makefile.am ++++ b/Makefile.am +@@ -1,440 +1,92 @@ + ACLOCAL_AMFLAGS = -I m4 + +-AM_CXXFLAGS = +-AM_CXXFLAGS += -Wall +-AM_CXXFLAGS += $(BOOST_CPPFLAGS) ++AM_CXXFLAGS = -Wall $(BOOST_CPPFLAGS) ++SUFFIXES = .cc + +- +-# for testing +-AM_CXXFLAGS += -g -O2 #-lefence +- +-# for profiling +-#CXXFLAGS += -O3 -g -pg +-#AM_CXXFLAGS += -O3 -g -pg +- +-# for production +-#CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +-#AM_CXXFLAGS += -O3 -fexpensive-optimizations -DNDEBUG +- +-# for coverage testing +-#CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +-#AM_CXXFLAGS += -g -fprofile-arcs -ftest-coverage -O3 -fexpensive-optimizations +- +- +-lib_LIBRARIES = libsnpfile.a ++lib_LTLIBRARIES = libsnpfile.la + + noinst_PROGRAMS = +-TESTS = +-EXTRA_DIST = +-bin_PROGRAMS = + + # conversion tools +-bin_PROGRAMS += text2snpfile +-bin_PROGRAMS += snpfile2text +-bin_PROGRAMS += snpfile2fastPHASE +-bin_PROGRAMS += fastPHASE2snpfile +-bin_PROGRAMS += snpfile2haploview +-bin_PROGRAMS += beagle_phase_snpfile ++bin_PROGRAMS = text2snpfile snpfile2text snpfile2fastPHASE fastPHASE2snpfile \ ++ snpfile2haploview beagle_phase_snpfile + + # data extraction tools +-bin_PROGRAMS += snpfile_genotype_count +-bin_PROGRAMS += snpfile_phenotypes +-bin_PROGRAMS += snpfile_markers +- +-bin_PROGRAMS += snpfile_metadata_info +-bin_PROGRAMS += snpfile_set_metadata +-bin_PROGRAMS += snpfile_get_metadata ++bin_PROGRAMS += snpfile_genotype_count snpfile_phenotypes snpfile_markers ++ ++bin_PROGRAMS += snpfile_metadata_info snpfile_set_metadata snpfile_get_metadata + + # other tools + noinst_PROGRAMS += snpfile_split_on_column + + # tests +-noinst_PROGRAMS += matrix_test +-TESTS += matrix_test +-noinst_PROGRAMS += file_test +-TESTS += file_test +-noinst_PROGRAMS += file_matrix_test +-TESTS += file_matrix_test +-noinst_PROGRAMS += readonly_matrix_test +-TESTS += readonly_matrix_test +-noinst_PROGRAMS += archives_test +-TESTS += archives_test +-noinst_PROGRAMS += metadata_access_test +-TESTS += metadata_access_test +-noinst_PROGRAMS += metadata_types_test +-TESTS += metadata_types_test +-noinst_PROGRAMS += iterators_test +-TESTS += iterators_test +-noinst_PROGRAMS += tabulate_test +-TESTS += tabulate_test +-noinst_PROGRAMS += metadata_filtering_test +-TESTS += metadata_filtering_test ++TESTS = matrix_test file_test file_matrix_test readonly_matrix_test archives_test \ ++ metadata_access_test metadata_types_test iterators_test tabulate_test metadata_filtering_test ++ ++noinst_PROGRAMS += $(TESTS) + + #Utils for testing across different machines +-noinst_PROGRAMS += make_test_snpfile +-noinst_PROGRAMS += test_test_snpfile ++noinst_PROGRAMS += make_test_snpfile test_test_snpfile + + # other experiments... +-noinst_PROGRAMS += row_metadata_experiment +-noinst_PROGRAMS += metadata_cache_prototype +-noinst_PROGRAMS += matrix_benchmark +-noinst_PROGRAMS += matrix_benchmark_write +-noinst_PROGRAMS += matrix_benchmark_read +- +- +- +-matrix_test_LDADD = +-matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_test_SOURCES = +-matrix_test_SOURCES += test_util.hh test_util.cc +-matrix_test_SOURCES += matrix.hh matrix.cc +-matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-matrix_test_SOURCES += input_archive.hh +-matrix_test_SOURCES += output_archive.hh +-matrix_test_SOURCES += metadata.hh metadata.cc +-matrix_test_SOURCES += snpfile.hh snpfile.cc +-matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_test_SOURCES += matrix_test.cc +- +- +-file_test_LDADD = +-file_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_test_SOURCES = +-file_test_SOURCES += test_util.hh test_util.cc +-file_test_SOURCES += metadata.hh metadata.cc +-file_test_SOURCES += snpfile.hh snpfile.cc +-file_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_test_SOURCES += file_test.cc +-file_test_SOURCES += metadata_access.hh +-file_test_SOURCES += input_archive.hh +-file_test_SOURCES += output_archive.hh +- +-file_matrix_test_LDADD = +-file_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-file_matrix_test_SOURCES = +-file_matrix_test_SOURCES += test_util.hh test_util.cc +-file_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-file_matrix_test_SOURCES += matrix.hh matrix.cc +-file_matrix_test_SOURCES += input_archive.hh +-file_matrix_test_SOURCES += output_archive.hh +-file_matrix_test_SOURCES += metadata.hh metadata.cc +-file_matrix_test_SOURCES += snpfile.hh snpfile.cc +-file_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-file_matrix_test_SOURCES += file_matrix_test.cc +- +- +-readonly_matrix_test_LDADD = +-readonly_matrix_test_LDADD += $(BOOST_SIGNALS_LIB) +-readonly_matrix_test_SOURCES = +-readonly_matrix_test_SOURCES += test_util.hh test_util.cc +-readonly_matrix_test_SOURCES += array_matrix.hh array_matrix.cc +-readonly_matrix_test_SOURCES += file_matrix.hh file_matrix.cc +-readonly_matrix_test_SOURCES += matrix.hh matrix.cc +-readonly_matrix_test_SOURCES += input_archive.hh +-readonly_matrix_test_SOURCES += output_archive.hh +-readonly_matrix_test_SOURCES += metadata.hh metadata.cc +-readonly_matrix_test_SOURCES += snpfile.hh snpfile.cc +-readonly_matrix_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-readonly_matrix_test_SOURCES += readonly_matrix_test.cc +- +- +-archives_test_SOURCES = +-archives_test_SOURCES += input_archive.hh +-archives_test_SOURCES += output_archive.hh +-archives_test_SOURCES += archives_test.cc +- +- +-metadata_access_test_LDADD = +-metadata_access_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_access_test_SOURCES = +-metadata_access_test_SOURCES += test_util.hh test_util.cc +-metadata_access_test_SOURCES += metadata.hh metadata.cc +-metadata_access_test_SOURCES += snpfile.hh snpfile.cc +-metadata_access_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_access_test_SOURCES += input_archive.hh +-metadata_access_test_SOURCES += output_archive.hh +-metadata_access_test_SOURCES += serialization_trait.hh +-metadata_access_test_SOURCES += metadata_access_test.cc +- +- +-metadata_types_test_LDADD = +-metadata_types_test_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_types_test_SOURCES = +-metadata_types_test_SOURCES += test_util.hh test_util.cc +-metadata_types_test_SOURCES += metadata.hh metadata.cc +-metadata_types_test_SOURCES += snpfile.hh snpfile.cc +-metadata_types_test_SOURCES += byte_order_handler.hh byte_order_handler.cc +-metadata_types_test_SOURCES += input_archive.hh +-metadata_types_test_SOURCES += output_archive.hh +-metadata_types_test_SOURCES += serialization_trait.hh +-metadata_types_test_SOURCES += metadata_types_test.cc +- +- +-iterators_test_SOURCES = +-iterators_test_SOURCES += iterators.hh +-iterators_test_SOURCES += array_matrix.hh array_matrix.cc +-iterators_test_SOURCES += matrix.hh matrix.cc +-iterators_test_SOURCES += iterators_test.cc +- +- +-tabulate_test_SOURCES = +-tabulate_test_SOURCES += tabulate.hh +-tabulate_test_SOURCES += array_matrix.hh array_matrix.cc +-tabulate_test_SOURCES += matrix.hh matrix.cc +-tabulate_test_SOURCES += tabulate_test.cc +- +- +-metadata_filtering_test_SOURCES = +-metadata_filtering_test_SOURCES += matrix.hh matrix.cc +-metadata_filtering_test_SOURCES += array_matrix.hh array_matrix.cc +-metadata_filtering_test_SOURCES += metadata_filtering.hh +-metadata_filtering_test_SOURCES += metadata_filtering_test.cc +- +- +-make_test_snpfile_LDADD = +-make_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-make_test_snpfile_SOURCES = +-make_test_snpfile_SOURCES += metadata.hh metadata.cc +-make_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-make_test_snpfile_SOURCES += matrix.hh matrix.cc +-make_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-make_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-make_test_snpfile_SOURCES += input_archive.hh +-make_test_snpfile_SOURCES += output_archive.hh +-make_test_snpfile_SOURCES += make_test_snpfile.cc +- +- +-test_test_snpfile_LDADD = +-test_test_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-test_test_snpfile_SOURCES = +-test_test_snpfile_SOURCES += metadata.hh metadata.cc +-test_test_snpfile_SOURCES += snpfile.hh snpfile.cc +-test_test_snpfile_SOURCES += matrix.hh matrix.cc +-test_test_snpfile_SOURCES += file_matrix.hh file_matrix.cc +-test_test_snpfile_SOURCES += byte_order_handler.hh byte_order_handler.cc +-test_test_snpfile_SOURCES += input_archive.hh +-test_test_snpfile_SOURCES += output_archive.hh +-test_test_snpfile_SOURCES += test_test_snpfile.cc +- +- +-row_metadata_experiment_LDADD = +-row_metadata_experiment_LDADD += $(BOOST_SIGNALS_LIB) +-row_metadata_experiment_SOURCES = +-row_metadata_experiment_SOURCES += matrix.hh matrix.cc +-row_metadata_experiment_SOURCES += array_matrix.hh array_matrix.cc +-row_metadata_experiment_SOURCES += file_matrix.hh file_matrix.cc +-row_metadata_experiment_SOURCES += input_archive.hh +-row_metadata_experiment_SOURCES += output_archive.hh +-row_metadata_experiment_SOURCES += metadata.hh metadata.cc +-row_metadata_experiment_SOURCES += snpfile.hh snpfile.cc +-row_metadata_experiment_SOURCES += byte_order_handler.hh byte_order_handler.cc +-row_metadata_experiment_SOURCES += test_util.hh test_util.cc +-row_metadata_experiment_SOURCES += row_metadata_experiment.cc +- +- +-metadata_cache_prototype_SOURCES = +-metadata_cache_prototype_SOURCES += metadata_cache_prototype.cc +-metadata_cache_prototype_LDFLAGS = +-metadata_cache_prototype_LDFLAGS += -L. +-metadata_cache_prototype_LDADD = +-metadata_cache_prototype_LDADD += $(BOOST_SIGNALS_LIB) +-metadata_cache_prototype_LDADD += -lsnpfile +- +- +-matrix_benchmark_LDADD = +-matrix_benchmark_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_SOURCES = +-matrix_benchmark_SOURCES += test_util.hh test_util.cc +-matrix_benchmark_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_SOURCES += array_matrix.hh array_matrix.cc +-matrix_benchmark_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_SOURCES += input_archive.hh +-matrix_benchmark_SOURCES += output_archive.hh +-matrix_benchmark_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_SOURCES += timing.hh timing.cc +-matrix_benchmark_SOURCES += matrix_benchmark.cc +- +- +-matrix_benchmark_write_LDADD = +-matrix_benchmark_write_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_write_SOURCES = +-matrix_benchmark_write_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_write_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_write_SOURCES += input_archive.hh +-matrix_benchmark_write_SOURCES += output_archive.hh +-matrix_benchmark_write_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_write_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_write_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_write_SOURCES += timing.hh timing.cc +-matrix_benchmark_write_SOURCES += matrix_benchmark_write.cc +- +- +-matrix_benchmark_read_LDADD = +-matrix_benchmark_read_LDADD += $(BOOST_SIGNALS_LIB) +-matrix_benchmark_read_SOURCES = +-matrix_benchmark_read_SOURCES += file_matrix.hh file_matrix.cc +-matrix_benchmark_read_SOURCES += matrix.hh matrix.cc +-matrix_benchmark_read_SOURCES += input_archive.hh +-matrix_benchmark_read_SOURCES += output_archive.hh +-matrix_benchmark_read_SOURCES += metadata.hh metadata.cc +-matrix_benchmark_read_SOURCES += snpfile.hh snpfile.cc +-matrix_benchmark_read_SOURCES += byte_order_handler.hh byte_order_handler.cc +-matrix_benchmark_read_SOURCES += timing.hh timing.cc +-matrix_benchmark_read_SOURCES += matrix_benchmark_read.cc ++noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ ++ matrix_benchmark_write matrix_benchmark_read ++ ++LDADD = $(top_builddir)/libsnpfile.la ++ ++matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc ++ ++file_test_SOURCES = test_util.hh test_util.cc file_test.cc metadata_access.hh input_archive.hh \ ++ output_archive.hh ++ ++file_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ file_matrix_test.cc ++ ++readonly_matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ readonly_matrix_test.cc + ++archives_test_SOURCES = input_archive.hh output_archive.hh archives_test.cc ++ ++metadata_access_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_access_test.cc ++ ++metadata_types_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh \ ++ serialization_trait.hh metadata_types_test.cc ++ ++iterators_test_SOURCES = iterators.hh iterators_test.cc ++ ++tabulate_test_SOURCES = tabulate.hh tabulate_test.cc ++ ++metadata_filtering_test_SOURCES = metadata_filtering.hh metadata_filtering_test.cc ++ ++make_test_snpfile_SOURCES = input_archive.hh output_archive.hh make_test_snpfile.cc ++ ++test_test_snpfile_SOURCES = input_archive.hh output_archive.hh test_test_snpfile.cc ++ ++row_metadata_experiment_SOURCES = input_archive.hh output_archive.hh test_util.hh test_util.cc \ ++ row_metadata_experiment.cc ++ ++matrix_benchmark_SOURCES = test_util.hh test_util.cc input_archive.hh \ ++ output_archive.hh timing.hh timing.cc matrix_benchmark.cc ++ ++matrix_benchmark_write_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_write.cc ++ ++matrix_benchmark_read_SOURCES = input_archive.hh output_archive.hh \ ++ timing.hh timing.cc matrix_benchmark_read.cc ++ ++snpfile_genotype_count_SOURCES = genotype_count.cc + + snpfileincludedir = $(includedir)/snpfile +-snpfileinclude_HEADERS = +-snpfileinclude_HEADERS += common.hh +-snpfileinclude_HEADERS += matrix.hh +-snpfileinclude_HEADERS += file_matrix.hh +-snpfileinclude_HEADERS += array_matrix.hh +-snpfileinclude_HEADERS += byte_order_handler.hh +-snpfileinclude_HEADERS += metadata.hh +-snpfileinclude_HEADERS += metadata_access.hh +-snpfileinclude_HEADERS += archive_common.hh +-snpfileinclude_HEADERS += archives.hh +-snpfileinclude_HEADERS += input_archive.hh +-snpfileinclude_HEADERS += output_archive.hh +-snpfileinclude_HEADERS += snpfile.hh +-snpfileinclude_HEADERS += serialization_trait.hh +-snpfileinclude_HEADERS += type_trait.hh +-snpfileinclude_HEADERS += iterators.hh +-snpfileinclude_HEADERS += tabulate.hh +- +-libsnpfile_a_SOURCES = +-libsnpfile_a_SOURCES += common.hh +-libsnpfile_a_SOURCES += matrix.hh matrix.cc +-libsnpfile_a_SOURCES += file_matrix.hh file_matrix.cc +-libsnpfile_a_SOURCES += array_matrix.cc array_matrix.hh +-libsnpfile_a_SOURCES += byte_order_handler.cc byte_order_handler.hh +-libsnpfile_a_SOURCES += metadata.hh metadata.cc metadata_access.hh +-libsnpfile_a_SOURCES += archive_common.hh +-libsnpfile_a_SOURCES += archives.hh +-libsnpfile_a_SOURCES += input_archive.hh +-libsnpfile_a_SOURCES += output_archive.hh +-libsnpfile_a_SOURCES += snpfile.hh snpfile.cc +-libsnpfile_a_SOURCES += serialization_trait.hh +-libsnpfile_a_SOURCES += type_trait.hh +- +-text2snpfile_SOURCES = +-text2snpfile_SOURCES += text2snpfile.cc +-text2snpfile_LDFLAGS = +-text2snpfile_LDFLAGS += -L. +-text2snpfile_LDADD = +-text2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-text2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-text2snpfile_LDADD += -lsnpfile +- +-snpfile2text_SOURCES = +-snpfile2text_SOURCES += snpfile2text.cc +-snpfile2text_LDFLAGS = +-snpfile2text_LDFLAGS += -L. +-snpfile2text_LDADD = +-snpfile2text_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2text_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2text_LDADD += -lsnpfile +- +- +-snpfile2fastPHASE_SOURCES = +-snpfile2fastPHASE_SOURCES += snpfile2fastPHASE.cc +-snpfile2fastPHASE_LDFLAGS = +-snpfile2fastPHASE_LDFLAGS += -L. +-snpfile2fastPHASE_LDADD = +-snpfile2fastPHASE_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2fastPHASE_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2fastPHASE_LDADD += -lsnpfile +- +-fastPHASE2snpfile_SOURCES = +-fastPHASE2snpfile_SOURCES += fastPHASE2snpfile.cc +-fastPHASE2snpfile_LDFLAGS = +-fastPHASE2snpfile_LDFLAGS += -L. +-fastPHASE2snpfile_LDADD = +-fastPHASE2snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-fastPHASE2snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-fastPHASE2snpfile_LDADD += -lsnpfile +- +- +-snpfile2haploview_SOURCES = +-snpfile2haploview_SOURCES += snpfile2haploview.cc +-snpfile2haploview_LDFLAGS = +-snpfile2haploview_LDFLAGS += -L. +-snpfile2haploview_LDADD = +-snpfile2haploview_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile2haploview_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile2haploview_LDADD += -lsnpfile +- +- +-beagle_phase_snpfile_SOURCES = +-beagle_phase_snpfile_SOURCES += beagle_phase_snpfile.cc +-beagle_phase_snpfile_LDFLAGS = +-beagle_phase_snpfile_LDFLAGS += -L. +-beagle_phase_snpfile_LDADD = +-beagle_phase_snpfile_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-beagle_phase_snpfile_LDADD += $(BOOST_SIGNALS_LIB) +-beagle_phase_snpfile_LDADD += -lsnpfile +- +-snpfile_genotype_count_SOURCES = +-snpfile_genotype_count_SOURCES += genotype_count.cc +-snpfile_genotype_count_LDFLAGS = +-snpfile_genotype_count_LDFLAGS += -L. +-snpfile_genotype_count_LDADD = +-snpfile_genotype_count_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_genotype_count_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_genotype_count_LDADD += -lsnpfile +- +-snpfile_phenotypes_SOURCES = +-snpfile_phenotypes_SOURCES += snpfile_phenotypes.cc +-snpfile_phenotypes_LDFLAGS = +-snpfile_phenotypes_LDFLAGS += -L. +-snpfile_phenotypes_LDADD = +-snpfile_phenotypes_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_phenotypes_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_phenotypes_LDADD += -lsnpfile +- +-snpfile_markers_SOURCES = +-snpfile_markers_SOURCES += snpfile_markers.cc +-snpfile_markers_LDFLAGS = +-snpfile_markers_LDFLAGS += -L. +-snpfile_markers_LDADD = +-snpfile_markers_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_markers_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_markers_LDADD += -lsnpfile +- +-snpfile_metadata_info_SOURCES = +-snpfile_metadata_info_SOURCES += snpfile_metadata_info.cc +-snpfile_metadata_info_LDFLAGS = +-snpfile_metadata_info_LDFLAGS += -L. +-snpfile_metadata_info_LDADD = +-snpfile_metadata_info_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_metadata_info_LDADD += -lsnpfile +- +-snpfile_set_metadata_SOURCES = +-snpfile_set_metadata_SOURCES += snpfile_set_metadata.cc +-snpfile_set_metadata_LDFLAGS = +-snpfile_set_metadata_LDFLAGS += -L. +-snpfile_set_metadata_LDADD = +-snpfile_set_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_set_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_set_metadata_LDADD += -lsnpfile +- +-snpfile_get_metadata_SOURCES = +-snpfile_get_metadata_SOURCES += snpfile_get_metadata.cc +-snpfile_get_metadata_LDFLAGS = +-snpfile_get_metadata_LDFLAGS += -L. +-snpfile_get_metadata_LDADD = +-snpfile_get_metadata_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_get_metadata_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_get_metadata_LDADD += -lsnpfile +- +-snpfile_split_on_column_SOURCES = +-snpfile_split_on_column_SOURCES += snpfile_split_on_column.cc +-snpfile_split_on_column_LDFLAGS = +-snpfile_split_on_column_LDFLAGS += -L. +-snpfile_split_on_column_LDADD = +-snpfile_split_on_column_LDADD += $(BOOST_PROGRAM_OPTIONS_LIB) +-snpfile_split_on_column_LDADD += $(BOOST_SIGNALS_LIB) +-snpfile_split_on_column_LDADD += -lsnpfile ++snpfileinclude_HEADERS = common.hh matrix.hh file_matrix.hh array_matrix.hh \ ++ byte_order_handler.hh metadata.hh metadata_access.hh archive_common.hh \ ++ archives.hh input_archive.hh output_archive.hh snpfile.hh serialization_trait.hh \ ++ type_trait.hh iterators.hh tabulate.hh ++ ++libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix.cc \ ++ array_matrix.cc array_matrix.hh byte_order_handler.cc byte_order_handler.hh \ ++ metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ ++ input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ ++ type_trait.hh ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++ +--- a/configure.in ++++ b/configure.in +@@ -1,10 +1,11 @@ + AC_INIT(snpfile, 2.0.1, mailund@birc.au.dk) + AM_INIT_AUTOMAKE ++AC_CONFIG_MACRO_DIR([m4]) + AM_CONFIG_HEADER(config.hh) + ++LT_INIT + AC_PROG_CXX + AC_PROG_INSTALL +-AC_PROG_RANLIB + + if test "x$prefix" != xNONE; then + thePREFIX=$prefix diff --git a/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch new file mode 100644 index 000000000000..2211aa36c0ca --- /dev/null +++ b/sci-biology/snpfile/files/snpfile-2.0.1-gold.patch @@ -0,0 +1,23 @@ + Makefile.am | 4 ++-- + 1 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/Makefile.am b/Makefile.am +index 06fd733..5805c48 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -32,7 +32,7 @@ noinst_PROGRAMS += make_test_snpfile test_test_snpfile + noinst_PROGRAMS += row_metadata_experiment metadata_cache_prototype matrix_benchmark \ + matrix_benchmark_write matrix_benchmark_read + +-LDADD = $(top_builddir)/libsnpfile.la ++LDADD = $(top_builddir)/libsnpfile.la $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + + matrix_test_SOURCES = test_util.hh test_util.cc input_archive.hh output_archive.hh matrix_test.cc + +@@ -88,5 +88,5 @@ libsnpfile_la_SOURCES = common.hh matrix.hh matrix.cc file_matrix.hh file_matrix + metadata.hh metadata.cc metadata_access.hh archive_common.hh archives.hh \ + input_archive.hh output_archive.hh snpfile.hh snpfile.cc serialization_trait.hh \ + type_trait.hh +-libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) ++libsnpfile_la_LIBADD = $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_SIGNALS_LIB) -lstdc++ + diff --git a/sci-biology/snpfile/metadata.xml b/sci-biology/snpfile/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/snpfile/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + diff --git a/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild new file mode 100644 index 000000000000..bbeb3111901f --- /dev/null +++ b/sci-biology/snpfile/snpfile-2.0.1-r2.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools + +DESCRIPTION="A library and API for manipulating large SNP datasets" +HOMEPAGE="http://www.birc.au.dk/~mailund/SNPFile/" +SRC_URI="http://www.birc.au.dk/~mailund/SNPFile/download/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="static-libs" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-libs/boost:=" +DEPEND=" + ${RDEPEND} + >=sys-devel/autoconf-archive-2016.09.16" + +PATCHES=( + "${FILESDIR}"/${P}-gcc44.patch + "${FILESDIR}"/${P}-gentoo.diff + "${FILESDIR}"/${P}-gold.patch + "${FILESDIR}"/${P}-ax-boost.patch +) + +src_prepare() { + default + mv configure.{in,ac} || die + rm m4/ax_boost.m4 || die + eautoreconf +} + +src_configure() { + econf $(use_enable static-libs static) +} + +src_install() { + default + + if ! use static-libs; then + find "${D}" -name '*.la' -delete || die + fi +} -- cgit v1.2.3