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-rw-r--r--sci-biology/kat/Manifest1
-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-2.4.2.ebuild83
-rw-r--r--sci-biology/kat/kat-9999.ebuild84
-rw-r--r--sci-biology/kat/metadata.xml15
6 files changed, 0 insertions, 318 deletions
diff --git a/sci-biology/kat/Manifest b/sci-biology/kat/Manifest
deleted file mode 100644
index 0bdd2dd15..000000000
--- a/sci-biology/kat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST kat-2.4.2.tar.gz 21829118 BLAKE2B 52a0056f322dfb405c005b31a0cb182c739a6af05173123dc1cef1d986f515a8318c1481f1ed0f8c247c01c6b460c951147d81f904709f4e27a7d3d1f47bda3d SHA512 696e3b9ed307ed17085790b24d617195f47fbdb7180be13ee644718c2464c429ffd964959857fc8d1317a451d57b74f6d7b2857fe3764573d9605d58a53b2a0c
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
deleted file mode 100644
index 46d343294..000000000
--- a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-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 \
-+ $(top_builddir)/lib/libkat.la \
- -lboost_timer \
- -lboost_chrono \
- -lboost_filesystem \
diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch
deleted file mode 100644
index 48ad6d562..000000000
--- a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-diff --git a/configure.ac b/configure.ac
-index 9acc141..24a4b14 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc)
-
- AM_CXXFLAGS="-g -O2 -std=c++11"
- AC_SUBST([AM_CXXFLAGS])
--AM_LDFLAGS="-static-libstdc++"
--AC_SUBST([AM_LDFLAGS])
-
- if [[ "${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 \
- $(top_builddir)/lib/libkat.la \
diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild
deleted file mode 100644
index a915d1491..000000000
--- a/sci-biology/kat/kat-2.4.2.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit autotools distutils-r1
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-SRC_URI="https://github.com/TGAC/KAT/archive/Release-${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[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="${CDEPEND}
- test? ( sys-process/time )"
-RDEPEND="${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}"
-
-distutils_enable_sphinx "${S}/doc/source" --no-autodoc
-distutils_enable_tests pytest
-
-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 ${myconf[@]}
-}
-
-src_compile(){
- default
- pushd scripts >/dev/null || die
- distutils-r1_src_compile
- popd > /dev/null || die
-}
-
-src_install(){
- default
- pushd scripts >/dev/null || die
- distutils-r1_src_install
- popd > /dev/null || die
-}
-
-src_test(){
- default
- python_foreach_impl python_test
-}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
deleted file mode 100644
index acbdac423..000000000
--- a/sci-biology/kat/kat-9999.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit autotools distutils-r1 git-r3
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT"
-EGIT_REPO_URI="https://github.com/TGAC/KAT.git"
-EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE="cpu_flags_x86_sse static-libs test"
-
-CDEPEND="
- >=dev-libs/boost-1.52[${PYTHON_USEDEP}]
- sys-libs/zlib
- dev-python/tabulate[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
-"
-DEPEND="${CDEPEND}
- test? ( sys-process/time )"
-RDEPEND="${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}"
-
-distutils_enable_sphinx "${S}/doc/source" --no-autodoc
-distutils_enable_tests pytest
-
-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
- python_foreach_impl python_test
-}
diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml
deleted file mode 100644
index 6810aabae..000000000
--- a/sci-biology/kat/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">TGAC/KAT</remote-id>
- </upstream>
-</pkgmetadata>