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-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
6 files changed, 193 insertions, 131 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 \