commit: f373141b6dd59db5eaf1bce4104e5ba6085958ac Author: François Bissey <frp.bissey <AT> gmail <DOT> com> AuthorDate: Mon Apr 23 08:51:16 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 7 21:44:57 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f373141b
sci-biology/kat: various fixes for issue #867 many thanks to @kiwifb and @maplesond for on fixing the package and ebuild ax_check_zlib is in use. A hint for zlib location has to be provided otherwise system zlib will be used on prefix. make sure zlib is a dependency. develop branch has switched to proper library detection. fixing rpath. enabling python support (but broken right now). make sure a suitable python3 is setup at configure time bump to 2.4.2 fix typo in /DEPPEND/DEPEND/, cleanup comments Closes: https://github.com/gentoo/sci/issues/867 Closes: https://github.com/gentoo/sci/pull/868 Package-Manager: Portage-2.3.31, Repoman-2.3.9 .../kat/files/kat-2.4.1-do-not-run-setup.py.patch | 30 ------ .../kat/files/kat-2.4.1-ignore-bundled-deps.patch | 101 --------------------- .../kat/files/kat-2.4.1-make_no_pykat.patch | 15 +++ .../kat/files/kat-2.4.1-no_static_build.patch | 43 +++++++++ .../kat/files/kat-2.4.2-ignore-bundled-deps.patch | 79 ++++++++++++++++ .../kat/files/kat-2.4.2-no_static_build.patch | 56 ++++++++++++ sci-biology/kat/kat-2.4.1.ebuild | 69 -------------- sci-biology/kat/kat-2.4.2.ebuild | 78 ++++++++++++++++ sci-biology/kat/kat-9999.ebuild | 60 +++++++----- sci-biology/kat/metadata.xml | 4 - 10 files changed, 307 insertions(+), 228 deletions(-) diff --git a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch deleted file mode 100644 index a00c971a6..000000000 --- a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- scripts/Makefile.am.ori 2018-04-22 16:02:12.829046527 +0200 -+++ scripts/Makefile.am 2018-04-22 16:05:31.444532061 +0200 -@@ -1,27 +1,6 @@ - AUTOMAKE_OPTIONS = subdir-objects - - --if MAKE_PYKAT_INSTALL -- --install-exec-hook: -- export PYTHONPATH=$(prefix)/lib/python$(PYTHON_VERSION)/site-packages && \ -- mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/site-packages/ && \ -- python3 setup.py install --prefix=$(prefix) --record install_files.txt -- --uninstall-hook: -- cat install_files.txt | xargs rm -rf -- --else -- --install-exec-hook: -- mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/local/ && \ -- cp -r kat $(prefix)/lib/python$(PYTHON_VERSION)/local -- --uninstall-hook: -- rm -rf $(prefix)/lib/python$(PYTHON_VERSION)/local -- --endif -- - EXTRA_DIST = \ - kat/distanalysis.py \ - kat/plot/__init__.py \ diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch deleted file mode 100644 index 649f3ecd8..000000000 --- a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch +++ /dev/null @@ -1,101 +0,0 @@ ---- configure.ac.ori 2018-04-22 12:19:37.318794996 +0200 -+++ configure.ac 2018-04-22 12:20:43.310663598 +0200 -@@ -172,8 +172,8 @@ - - - AC_CONFIG_HEADERS([config.h]) --AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc lib/Makefile src/Makefile tests/Makefile tests/compat.sh deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py scripts/Makefile]) --AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0]) -+AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc lib/Makefile src/Makefile tests/Makefile tests/compat.sh deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py scripts/Makefile]) -+AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0]) - AC_OUTPUT - - pystr="detected ${PYTHON_VERSION}. Plotting and downstream analysis enabled." ---- lib/Makefile.am.ori 2018-04-22 15:30:34.983653065 +0200 -+++ lib/Makefile.am 2018-04-22 15:30:46.143961300 +0200 -@@ -7,8 +7,7 @@ - - libkat_la_LDFLAGS = \ - -version-info 2:4:0 \ -- -L../deps/jellyfish-2.2.0 \ -- -L../deps/boost/build/lib -+ -L../deps/jellyfish-2.2.0 - - libkat_la_SOURCES = \ - src/matrix_metadata_extractor.cc \ -@@ -31,7 +30,6 @@ - - libkat_la_CPPFLAGS = \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ ---- src/Makefile.am.ori 2018-04-22 15:30:46.203962959 +0200 -+++ src/Makefile.am 2018-04-22 15:31:41.385487008 +0200 -@@ -14,7 +14,6 @@ - kat_CPPFLAGS = \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -@@ -23,17 +22,16 @@ - -static \ - -L../lib \ - -L../deps/jellyfish-2.2.0 \ -- -L../deps/boost/build/lib \ - @AM_LDFLAGS@ - - kat_LDADD = \ - -lkat \ - -lkat_jellyfish \ -- ../deps/boost/build/lib/libboost_timer.a \ -- ../deps/boost/build/lib/libboost_chrono.a \ -- ../deps/boost/build/lib/libboost_filesystem.a \ -- ../deps/boost/build/lib/libboost_program_options.a \ -- ../deps/boost/build/lib/libboost_system.a \ -+ -lboost_timer \ -+ -lboost_chrono \ -+ -lboost_filesystem \ -+ -lboost_program_options \ -+ -lboost_system \ - @AM_LIBS@ - - noinst_HEADERS = \ ---- tests/Makefile.am.ori 2018-04-22 15:31:41.505490322 +0200 -+++ tests/Makefile.am 2018-04-22 15:32:37.787044756 +0200 -@@ -31,7 +31,6 @@ - -I$(top_srcdir)/lib/include \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -DDATADIR=\"$(srcdir)/data\" \ - -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -@@ -61,7 +60,6 @@ - -L. \ - -L../lib \ - -L../deps/jellyfish-2.2.0 \ -- -L../deps/boost/build/lib \ - @AM_LDFLAGS@ - - check_unit_tests_LDADD = \ -@@ -69,11 +67,11 @@ - -lgtest \ - -lkat \ - -lkat_jellyfish \ -- ../deps/boost/build/lib/libboost_timer.a \ -- ../deps/boost/build/lib/libboost_chrono.a \ -- ../deps/boost/build/lib/libboost_filesystem.a \ -- ../deps/boost/build/lib/libboost_program_options.a \ -- ../deps/boost/build/lib/libboost_system.a \ -+ -lboost_timer \ -+ -lboost_chrono \ -+ -lboost_filesystem \ -+ -lboost_program_options \ -+ -lboost_system \ - @AM_LIBS@ - - include gtest.mk diff --git a/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch b/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch new file mode 100644 index 000000000..7ba08010c --- /dev/null +++ b/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch @@ -0,0 +1,15 @@ +diff --git a/Makefile.am b/Makefile.am +index 5f0f42e..4da6c05 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -21,10 +21,6 @@ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh + # SRC DIRS + make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests + +-if MAKE_PYKAT +- make_dirs += scripts +-endif +- + if MAKE_DOCS + make_dirs += doc + endif diff --git a/sci-biology/kat/files/kat-2.4.1-no_static_build.patch b/sci-biology/kat/files/kat-2.4.1-no_static_build.patch new file mode 100644 index 000000000..c8ac6c901 --- /dev/null +++ b/sci-biology/kat/files/kat-2.4.1-no_static_build.patch @@ -0,0 +1,43 @@ +diff --git a/configure.ac b/configure.ac +index b68c514..00c8a2e 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -159,11 +159,11 @@ if [[ "${make_pykat}" == "yes" ]]; then + AM_CPPFLAGS="${ZLIB_CPPFLAGS} ${PYTHON_CPPFLAGS}" + AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB} ${PYTHON_EXTRA_LIBS} ${PYTHON_LIBS}" + #AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_EXTRA_LDFLAGS} ${PYTHON_RPATH} -static-libstdc++" +- AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++ ${PYTHON_RPATH}" ++ AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_RPATH}" + else + AM_CPPFLAGS="${ZLIB_CPPFLAGS}" + AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB}" +- AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++" ++ AM_LDFLAGS="${ZLIB_LDFLAGS}" + fi + + AC_SUBST([AM_CPPFLAGS]) +diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am +index 8f6fffd..d6e0a3d 100644 +--- a/deps/jellyfish-2.2.0/Makefile.am ++++ b/deps/jellyfish-2.2.0/Makefile.am +@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man + pkgconfigdir = $(libdir)/pkgconfig + pkgconfig_DATA = kat_jellyfish.pc + +-AM_LDFLAGS = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread -static-libstdc++ # $(VALGRIND_LIBS) ++AM_LDFLAGS = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread # $(VALGRIND_LIBS) + AM_CPPFLAGS = $(ZLIB_CPPFLAGS) -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS) + AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations + +diff --git a/src/Makefile.am b/src/Makefile.am +index a2ae071..71def5c 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -19,7 +19,6 @@ kat_CPPFLAGS = \ + @AM_CPPFLAGS@ + + kat_LDFLAGS = \ +- -static \ + @AM_LDFLAGS@ + + kat_LDADD = \ diff --git a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch new file mode 100644 index 000000000..46d343294 --- /dev/null +++ b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch @@ -0,0 +1,79 @@ +diff --git a/lib/Makefile.am b/lib/Makefile.am +index ac23917..0ca4be9 100644 +--- a/lib/Makefile.am ++++ b/lib/Makefile.am +@@ -6,7 +6,6 @@ pkgconfig_DATA = kat.pc + lib_LTLIBRARIES = libkat.la + + libkat_la_LDFLAGS = \ +- -L$(top_builddir)/deps/boost/build/lib/ \ + -version-info 2:4:2 + + LIBS = \ +@@ -41,7 +40,6 @@ library_include_HEADERS = $(KI)/distance_metrics.hpp \ + + libkat_la_CPPFLAGS = \ + -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ +- -I$(top_srcdir)/deps/boost/build/include \ + -I$(top_srcdir)/lib/include \ + -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ + @AM_CPPFLAGS@ +diff --git a/src/Makefile.am b/src/Makefile.am +index 1cdf7e0..dfa878b 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -14,7 +14,6 @@ kat_CXXFLAGS = \ + kat_CPPFLAGS = \ + -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ + -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ +- -I$(top_srcdir)/deps/boost/build/include \ + -I$(top_srcdir)/lib/include \ + -DKAT_SCRIPTS='"$(datarootdir)/scripts"' \ + -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ +@@ -25,13 +24,13 @@ kat_LDFLAGS = \ + @AM_LDFLAGS@ + + kat_LDADD = \ +- $(top_builddir)/deps/boost/build/lib/libboost_timer.a \ +- $(top_builddir)/deps/boost/build/lib/libboost_chrono.a \ +- $(top_builddir)/deps/boost/build/lib/libboost_filesystem.a \ +- $(top_builddir)/deps/boost/build/lib/libboost_program_options.a \ +- $(top_builddir)/deps/boost/build/lib/libboost_system.a \ +- $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ + $(top_builddir)/lib/libkat.la \ ++ $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ ++ -lboost_timer \ ++ -lboost_chrono \ ++ -lboost_filesystem \ ++ -lboost_program_options \ ++ -lboost_system \ + @AM_LIBS@ + + noinst_HEADERS = \ +diff --git a/tests/Makefile.am b/tests/Makefile.am +index eee4e8b..dec2a5f 100644 +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -31,7 +31,6 @@ AM_CPPFLAGS = \ + -I$(top_srcdir)/lib/include \ + -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ + -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ +- -I$(top_srcdir)/deps/boost/build/include \ + -DDATADIR=\"$(srcdir)/data\" \ + -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ + @AM_CPPFLAGS@ +@@ -58,13 +57,11 @@ check_unit_tests_SOURCES = \ + + check_unit_tests_LDFLAGS = \ + -static \ +- -L$(top_builddir)/deps/boost/build/lib \ +- -Wl,-rpath $(top_builddir)/deps/boost/build/lib \ + @AM_LDFLAGS@ + + check_unit_tests_LDADD = \ + libgtest.la \ +- $(top_builddir)/lib/libkat.la \ ++ $(top_builddir)/lib/libkat.la \ + -lboost_timer \ + -lboost_chrono \ + -lboost_filesystem \ diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch new file mode 100644 index 000000000..48ad6d562 --- /dev/null +++ b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch @@ -0,0 +1,56 @@ +diff --git a/configure.ac b/configure.ac +index 9acc141..24a4b14 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc) + + AM_CXXFLAGS="-g -O2 -std=c++11" + AC_SUBST([AM_CXXFLAGS]) +-AM_LDFLAGS="-static-libstdc++" +-AC_SUBST([AM_LDFLAGS]) + + if [[ "${make_pykat}" == "yes" ]]; then + AM_CPPFLAGS="${PYTHON_CPPFLAGS}" +diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am +index 83192d9..e3b1694 100644 +--- a/deps/jellyfish-2.2.0/Makefile.am ++++ b/deps/jellyfish-2.2.0/Makefile.am +@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man + pkgconfigdir = $(libdir)/pkgconfig + pkgconfig_DATA = kat_jellyfish.pc + +-AM_LDFLAGS = -lz -lpthread -static-libstdc++ # $(VALGRIND_LIBS) ++AM_LDFLAGS = -lz -lpthread # $(VALGRIND_LIBS) + AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS) + AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations + +diff --git a/src/Makefile.am b/src/Makefile.am +index 2d5cd72..cb5cb0e 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -18,10 +18,6 @@ kat_CPPFLAGS = \ + -DKAT_SCRIPTS='"$(datadir)/scripts"' \ + @AM_CPPFLAGS@ + +-kat_LDFLAGS = \ +- -static \ +- @AM_LDFLAGS@ +- + kat_LDADD = \ + $(top_builddir)/lib/libkat.la \ + $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ +diff --git a/tests/Makefile.am b/tests/Makefile.am +index d96363a..90e4f61 100644 +--- a/tests/Makefile.am ++++ b/tests/Makefile.am +@@ -54,10 +54,6 @@ check_unit_tests_SOURCES = \ + check_compcounters.cc \ + check_main.cc + +-check_unit_tests_LDFLAGS = \ +- -static \ +- @AM_LDFLAGS@ +- + check_unit_tests_LDADD = \ + libgtest.la \ + $(top_builddir)/lib/libkat.la \ diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild deleted file mode 100644 index 3bd8b7dde..000000000 --- a/sci-biology/kat/kat-2.4.1.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 -# https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit eutils flag-o-matic autotools distutils-r1 - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT"; -SRC_URI="https://github.com/TGAC/KAT/archive/Release-2.4.1.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cpu_flags_x86_sse doc tex" - -DEPEND=" - >=dev-libs/boost-1.52[${PYTHON_USEDEP}] - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) - tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )" -RDEPEND="${DEPEND}" -# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) -# contains embedded sci-biology/seqan - -S="${WORKDIR}"/KAT-Release-"${PV}" - -src_prepare(){ - default - # keep bundled seqan-library-2.0.0 jellyfish-2.2.0 - # seqan header do not hurt - # jellyfish-2.2.0 is a modified version, "kat_" prefixes are added to all binaries - # https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 - rm -rf deps/boost || die "Failed to zap bundled boost" - epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch - epatch "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch - eautoreconf - pushd scripts >/dev/null || die - distutils-r1_src_prepare - popd > /dev/null || die -} - -src_configure(){ - local myconf=() - myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.2.0/configure - econf ${myconf[@]} -} - -src_compile(){ - emake - cd doc && make latexpdf && cd .. || die - pushd scripts >/dev/null || die - distutils-r1_src_compile - popd > /dev/null || die -} - -src_install(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_install - popd > /dev/null || die -} diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild new file mode 100644 index 000000000..9d3981439 --- /dev/null +++ b/sci-biology/kat/kat-2.4.2.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python3_{5,6} ) +# https://github.com/Ensembl/Bio-DB-HTS/issues/30 + +inherit flag-o-matic autotools distutils-r1 + +DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" +HOMEPAGE="https://github.com/TGAC/KAT"; +SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse static-libs test" + +CDEPEND=" + >=dev-libs/boost-1.52[${PYTHON_USEDEP}] + sys-libs/zlib + dev-python/tabulate[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND="${CDEPEND} + dev-python/sphinx + test? ( sys-process/time )" +RDEPEND="${CDEPEND}" +# contains bundled and *modified* version of jellyfish-2.2.0 +# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) +# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 +# contains embedded sci-biology/seqan headers + +PATCHES=( + "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch + "${FILESDIR}"/kat-2.4.2-no_static_build.patch + ) + +S="${WORKDIR}"/KAT-Release-"${PV}" + +src_prepare(){ + default + rm -rf deps/boost || die "Failed to zap bundled boost" + eautoreconf +} + +src_configure(){ + python_setup + local myconf=() + myconf+=( + --disable-gnuplot + --disable-pykat-install + $(use_enable static-libs static) + ) # python3 does better image rendering, no need for gnuplot + # pass down to jellyfish-2.2.0/configure + use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) + econf ${myconf[@]} +} + +src_compile(){ + default + pushd scripts >/dev/null || die + distutils-r1_src_compile + popd > /dev/null || die +} + +src_install(){ + default + pushd scripts >/dev/null || die + distutils-r1_src_install + popd > /dev/null || die +} + +src_test(){ + default +} diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild index 0ccec1481..aaf8842ba 100644 --- a/sci-biology/kat/kat-9999.ebuild +++ b/sci-biology/kat/kat-9999.ebuild @@ -3,57 +3,65 @@ EAPI=6 -PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 +PYTHON_COMPAT=( python3_{5,6} ) # https://github.com/Ensembl/Bio-DB-HTS/issues/30 -inherit git-r3 eutils flag-o-matic autotools distutils-r1 +inherit flag-o-matic autotools distutils-r1 git-r3 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" HOMEPAGE="https://github.com/TGAC/KAT"; EGIT_REPO_URI="https://github.com/TGAC/KAT.git"; +EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}" LICENSE="GPL-3+" SLOT="0" -KEYWORDS="" -IUSE="cpu_flags_x86_sse doc tex" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_x86_sse static-libs test" -DEPEND=" +CDEPEND=" >=dev-libs/boost-1.52[${PYTHON_USEDEP}] + sys-libs/zlib dev-python/tabulate[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) - tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )" -RDEPEND="${DEPEND}" -# contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) -# contains embedded sci-biology/seqan + sci-libs/scipy[${PYTHON_USEDEP}]" +DEPEND="${CDEPEND} + dev-python/sphinx + test? ( sys-process/time )" +RDEPEND="${CDEPEND}" +# contains bundled and *modified* version of jellyfish-2.2.0 +# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) +# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 +# contains embedded sci-biology/seqan headers + +PATCHES=( + "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch + "${FILESDIR}"/kat-2.4.2-no_static_build.patch + ) + +S="${WORKDIR}"/KAT-Release-"${PV}" src_prepare(){ default - # keep bundled seqan-library-2.0.0 jellyfish-2.2.0 - # seqan header do not hurt - # jellyfish-2.2.0 is a modified version, "kat_" prefixes are added to all binaries - # https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 rm -rf deps/boost || die "Failed to zap bundled boost" - epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch - epatch "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch eautoreconf - pushd scripts >/dev/null || die - distutils-r1_src_prepare - popd > /dev/null || die } src_configure(){ + python_setup local myconf=() - myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.2.0/configure + myconf+=( + --disable-gnuplot + --disable-pykat-install + $(use_enable static-libs static) + ) # python3 does better image rendering, no need for gnuplot + # pass down to jellyfish-2.2.0/configure + use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) econf ${myconf[@]} } src_compile(){ - emake - cd doc && make latexpdf && cd .. || die + default pushd scripts >/dev/null || die distutils-r1_src_compile popd > /dev/null || die @@ -65,3 +73,7 @@ src_install(){ distutils-r1_src_install popd > /dev/null || die } + +src_test(){ + default +} diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml index eb95c0c06..6810aabae 100644 --- a/sci-biology/kat/metadata.xml +++ b/sci-biology/kat/metadata.xml @@ -12,8 +12,4 @@ <upstream> <remote-id type="github">TGAC/KAT</remote-id> </upstream> - <use> - <flag name="doc">Enable building of .html from .rst documentation</flag> - <flag name="tex">Enable building of .pdf documentation from .rst via .tex intermediate</flag> - </use> </pkgmetadata>
