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authorFran├žois Bissey <frp.bissey@gmail.com>2018-04-23 20:51:16 +1200
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-05-07 23:44:57 +0200
commitf373141b6dd59db5eaf1bce4104e5ba6085958ac (patch)
tree91f81c87e9cc3439e07c5503e2368580ffd3289e
parentsci-libs/tensorflow: Move our flags to bazel-get-flags() (diff)
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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
-rw-r--r--sci-biology/kat/Manifest2
-rw-r--r--sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch30
-rw-r--r--sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch101
-rw-r--r--sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch15
-rw-r--r--sci-biology/kat/files/kat-2.4.1-no_static_build.patch43
-rw-r--r--sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch79
-rw-r--r--sci-biology/kat/files/kat-2.4.2-no_static_build.patch56
-rw-r--r--sci-biology/kat/kat-2.4.1.ebuild69
-rw-r--r--sci-biology/kat/kat-2.4.2.ebuild78
-rw-r--r--sci-biology/kat/kat-9999.ebuild60
-rw-r--r--sci-biology/kat/metadata.xml4
11 files changed, 308 insertions, 229 deletions
diff --git a/sci-biology/kat/Manifest b/sci-biology/kat/Manifest
index c6c41e19f..0bdd2dd15 100644
--- a/sci-biology/kat/Manifest
+++ b/sci-biology/kat/Manifest
@@ -1 +1 @@
-DIST kat-2.4.1.tar.gz 21833145 BLAKE2B 4812b0f8c450a3e851853b57efb8c4d4cfcb13fab685c7b12437f924938cf65bbfa5183cc928dbcfa4fa94f8b989688b24e68a287f8a4d0baa2fd351725f491d SHA512 54961f753e14f39a82a98cb64c387129f5251c2496e38f507f31d9fc945beb40cf900b75a54bcb9813850f9f4815c574bf41671fe047344792884a80caed5ad0
+DIST kat-2.4.2.tar.gz 21829118 BLAKE2B 52a0056f322dfb405c005b31a0cb182c739a6af05173123dc1cef1d986f515a8318c1481f1ed0f8c247c01c6b460c951147d81f904709f4e27a7d3d1f47bda3d SHA512 696e3b9ed307ed17085790b24d617195f47fbdb7180be13ee644718c2464c429ffd964959857fc8d1317a451d57b74f6d7b2857fe3764573d9605d58a53b2a0c
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>