* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/files/, sci-biology/kat/
@ 2018-04-22 11:45 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2018-04-22 11:45 UTC (permalink / raw
To: gentoo-commits
commit: 8ee8fd95880516f79f8693c728d0ec218fa82277
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 11:45:10 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 11:45:10 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ee8fd95
sci-biology/kat: ignore site-wide boost-build/site-config.jam
Introduce -8888 ebuild which zaps bundled stuff altogether and uses
system-wide boost and jellyfish2 files.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
.../kat/files/kat-2.4.1-ignore-bundled-deps.patch | 120 ++++++++++++++++
.../kat/files/kat-2.4.1-rename-jellyfish.patch | 159 +++++++++++++++++++++
sci-biology/kat/kat-2.4.1.ebuild | 7 +-
.../kat/{kat-9999.ebuild => kat-8888.ebuild} | 23 +--
sci-biology/kat/kat-9999.ebuild | 7 +-
5 files changed, 300 insertions(+), 16 deletions(-)
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
new file mode 100644
index 000000000..d1816498e
--- /dev/null
+++ b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
@@ -0,0 +1,120 @@
+--- 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 scripts/setup.py scripts/kat/__init__.py scripts/Makefile])
++AC_CONFIG_SUBDIRS([])
+ AC_OUTPUT
+
+ pystr="detected ${PYTHON_VERSION}. Plotting and downstream analysis enabled."
+--- Makefile.am.ori 2018-04-22 12:23:58.756197763 +0200
++++ Makefile.am 2018-04-22 12:24:21.176832618 +0200
+@@ -19,7 +19,7 @@
+ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
+
+ # SRC DIRS
+-make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
++make_dirs=lib src tests
+
+ if MAKE_PYKAT
+ make_dirs += scripts
+--- tests/Makefile.am.ori 2018-04-22 12:31:02.738203085 +0200
++++ tests/Makefile.am 2018-04-22 12:34:15.043648336 +0200
+@@ -29,8 +29,7 @@
+
+ AM_CPPFLAGS = \
+ -I$(top_srcdir)/lib/include \
+- -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
+- -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
++ -I$(top_srcdir)/usr/include/seqan-2.2 \
+ -I$(top_srcdir)/deps/boost/build/include \
+ -DDATADIR=\"$(srcdir)/data\" \
+ -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+@@ -60,7 +59,6 @@
+ -static \
+ -L. \
+ -L../lib \
+- -L../deps/jellyfish-2.2.0 \
+ -L../deps/boost/build/lib \
+ @AM_LDFLAGS@
+
+@@ -69,11 +67,11 @@
+ -lgtest \
+ -lkat \
+ -lkat_jellyfish \
+- ../deps/boost/build/lib/libboost_timer.a \
+- ../deps/boost/build/lib/libboost_chrono.a \
+- ../deps/boost/build/lib/libboost_filesystem.a \
+- ../deps/boost/build/lib/libboost_program_options.a \
+- ../deps/boost/build/lib/libboost_system.a \
++ -lboost_timer \
++ -lboost_chrono \
++ -lboost_filesystem \
++ -lboost_program_options \
++ -lboost_system \
+ @AM_LIBS@
+
+ include gtest.mk
+--- src/Makefile.am.ori 2018-04-22 12:34:41.874408065 +0200
++++ src/Makefile.am 2018-04-22 12:36:33.567570728 +0200
+@@ -12,9 +12,7 @@
+ @AM_CXXFLAGS@
+
+ kat_CPPFLAGS = \
+- -I$(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/usr/include/seqan-2.2 \
+ -I$(top_srcdir)/lib/include \
+ -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+ @AM_CPPFLAGS@
+@@ -22,18 +20,16 @@
+ kat_LDFLAGS = \
+ -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 = \
+--- lib/Makefile.am.ori 2018-04-22 12:38:29.680858551 +0200
++++ lib/Makefile.am 2018-04-22 12:38:58.401671799 +0200
+@@ -6,9 +6,7 @@
+ lib_LTLIBRARIES = libkat.la
+
+ libkat_la_LDFLAGS = \
+- -version-info 2:4:0 \
+- -L../deps/jellyfish-2.2.0 \
+- -L../deps/boost/build/lib
++ -version-info 2:4:0
+
+ libkat_la_SOURCES = \
+ src/matrix_metadata_extractor.cc \
+@@ -30,8 +28,6 @@
+ $(KI)/comp_counters.hpp
+
+ libkat_la_CPPFLAGS = \
+- -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
+- -I$(top_srcdir)/deps/boost/build/include \
+ -I$(top_srcdir)/lib/include \
+ -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+ @AM_CPPFLAGS@
diff --git a/sci-biology/kat/files/kat-2.4.1-rename-jellyfish.patch b/sci-biology/kat/files/kat-2.4.1-rename-jellyfish.patch
new file mode 100644
index 000000000..81d4f7d18
--- /dev/null
+++ b/sci-biology/kat/files/kat-2.4.1-rename-jellyfish.patch
@@ -0,0 +1,159 @@
+--- lib/include/kat/jellyfish_helper.hpp.ori 2018-04-22 12:47:42.296506217 +0200
++++ lib/include/kat/jellyfish_helper.hpp 2018-04-22 12:49:22.209335310 +0200
+@@ -41,18 +41,18 @@
+ using boost::lexical_cast;
+ using boost::timer::auto_cpu_timer;
+
+-#include <jellyfish/err.hpp>
+-#include <jellyfish/file_header.hpp>
+-#include <jellyfish/hash_counter.hpp>
+-#include <jellyfish/mapped_file.hpp>
+-#include <jellyfish/mer_dna.hpp>
+-#include <jellyfish/jellyfish.hpp>
+-#include <jellyfish/large_hash_array.hpp>
+-#include <jellyfish/large_hash_iterator.hpp>
+-#include <jellyfish/mer_iterator.hpp>
+-#include <jellyfish/mer_overlap_sequence_parser.hpp>
+-#include <jellyfish/storage.hpp>
+-#include <jellyfish/stream_manager.hpp>
++#include <jellyfish2/err.hpp>
++#include <jellyfish2/file_header.hpp>
++#include <jellyfish2/hash_counter.hpp>
++#include <jellyfish2/mapped_file.hpp>
++#include <jellyfish2/mer_dna.hpp>
++#include <jellyfish2/jellyfish.hpp>
++#include <jellyfish2/large_hash_array.hpp>
++#include <jellyfish2/large_hash_iterator.hpp>
++#include <jellyfish2/mer_iterator.hpp>
++#include <jellyfish2/mer_overlap_sequence_parser.hpp>
++#include <jellyfish2/storage.hpp>
++#include <jellyfish2/stream_manager.hpp>
+ using jellyfish::mer_dna;
+ using jellyfish::file_header;
+ using jellyfish::mapped_file;
+--- lib/src/jellyfish_helper.cc.ori 2018-04-22 12:47:50.166729065 +0200
++++ lib/src/jellyfish_helper.cc 2018-04-22 12:49:28.379510022 +0200
+@@ -35,15 +35,15 @@
+ using boost::lexical_cast;
+ using boost::timer::auto_cpu_timer;
+
+-#include <jellyfish/binary_dumper.hpp>
+-#include <jellyfish/err.hpp>
+-#include <jellyfish/file_header.hpp>
+-#include <jellyfish/mapped_file.hpp>
+-#include <jellyfish/mer_dna.hpp>
+-#include <jellyfish/jellyfish.hpp>
+-#include <jellyfish/large_hash_array.hpp>
+-#include <jellyfish/large_hash_iterator.hpp>
+-#include <jellyfish/storage.hpp>
++#include <jellyfish2/binary_dumper.hpp>
++#include <jellyfish2/err.hpp>
++#include <jellyfish2/file_header.hpp>
++#include <jellyfish2/mapped_file.hpp>
++#include <jellyfish2/mer_dna.hpp>
++#include <jellyfish2/jellyfish.hpp>
++#include <jellyfish2/large_hash_array.hpp>
++#include <jellyfish2/large_hash_iterator.hpp>
++#include <jellyfish2/storage.hpp>
+ using jellyfish::large_hash::reprobe_limit_t;
+ using jellyfish::Offsets;
+ using jellyfish::quadratic_reprobes;
+--- src/sect.cc.ori 2018-04-22 12:47:57.906948236 +0200
++++ src/sect.cc 2018-04-22 12:49:33.479654437 +0200
+@@ -53,7 +53,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/jellyfish_helper.hpp>
+ #include <kat/matrix_metadata_extractor.hpp>
+--- src/histogram.cc.ori 2018-04-22 12:48:06.427189490 +0200
++++ src/histogram.cc 2018-04-22 12:49:37.719774498 +0200
+@@ -44,7 +44,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/matrix_metadata_extractor.hpp>
+ #include <kat/jellyfish_helper.hpp>
+--- src/sect.hpp.ori 2018-04-22 12:48:13.167380343 +0200
++++ src/sect.hpp 2018-04-22 12:49:41.549882951 +0200
+@@ -45,7 +45,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/matrix_metadata_extractor.hpp>
+ #include <kat/jellyfish_helper.hpp>
+--- src/gcp.cc.ori 2018-04-22 12:48:20.457586772 +0200
++++ src/gcp.cc 2018-04-22 12:49:45.469993952 +0200
+@@ -44,7 +44,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/jellyfish_helper.hpp>
+ #include <kat/sparse_matrix.hpp>
+--- src/comp.cc.ori 2018-04-22 12:48:28.447813020 +0200
++++ src/comp.cc 2018-04-22 12:49:50.720142612 +0200
+@@ -48,7 +48,7 @@
+ namespace bfs = boost::filesystem;
+ using bfs::path;
+
+-#include <jellyfish/large_hash_iterator.hpp>
++#include <jellyfish2/large_hash_iterator.hpp>
+
+ #include <kat/matrix_metadata_extractor.hpp>
+ #include <kat/sparse_matrix.hpp>
+--- src/cold.cc.ori 2018-04-22 12:27:18.151843779 +0200
++++ src/cold.cc 2018-04-22 12:27:35.482334502 +0200
+@@ -53,7 +53,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/jellyfish_helper.hpp>
+ #include <kat/matrix_metadata_extractor.hpp>
+--- src/comp.hpp.ori 2018-04-22 12:27:53.022831172 +0200
++++ src/comp.hpp 2018-04-22 12:28:10.173316799 +0200
+@@ -33,7 +33,7 @@
+ namespace bfs = boost::filesystem;
+ using bfs::path;
+
+-#include <jellyfish/large_hash_iterator.hpp>
++#include <jellyfish2/large_hash_iterator.hpp>
+
+ #include <kat/matrix_metadata_extractor.hpp>
+ #include <kat/sparse_matrix.hpp>
+--- src/cold.hpp.ori 2018-04-22 12:29:23.725399473 +0200
++++ src/cold.hpp 2018-04-22 12:29:33.885687168 +0200
+@@ -45,7 +45,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/matrix_metadata_extractor.hpp>
+ #include <kat/jellyfish_helper.hpp>
+--- src/gcp.hpp.ori 2018-04-22 12:30:06.576612834 +0200
++++ src/gcp.hpp 2018-04-22 12:30:13.056796324 +0200
+@@ -36,7 +36,7 @@
+ using bfs::path;
+ using boost::lexical_cast;
+
+-#include <jellyfish/mer_dna.hpp>
++#include <jellyfish2/mer_dna.hpp>
+
+ #include <kat/pyhelper.hpp>
+ #include <kat/jellyfish_helper.hpp>
diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 1df9f4430..f1635e9e8 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -41,7 +41,7 @@ src_prepare(){
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-2.20/configure
+ use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.2.0/configure
PYTHON_VERSION=3 econf ${myconf[@]}
}
@@ -49,7 +49,8 @@ src_compile(){
# build_boost.sh
cd deps/boost || die
./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
- ./b2 headers || die
- ./b2 install || die
+ # https://github.com/TGAC/KAT/issues/92#issuecomment-383373418
+ ./b2 headers --ignore-site-config || die
+ ./b2 install --ignore-site-config || die
cd ../.. || die
}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-8888.ebuild
similarity index 67%
copy from sci-biology/kat/kat-9999.ebuild
copy to sci-biology/kat/kat-8888.ebuild
index d46f6d3e8..c59669fc5 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-8888.ebuild
@@ -30,9 +30,12 @@ RDEPEND="${DEPEND}"
src_prepare(){
default
+ rm -rf deps || die "Failed to zap bundled seqan-library-2.0.0 jellyfish-2.2.0 boost"
+ epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch
+ epatch "${FILESDIR}"/kat-2.4.1-rename-jellyfish.patch
# autogen.sh
- test -n "$srcdir" || local srcdir=`dirname "$0"`
- test -n "$srcdir" || local srcdir=.
+ #test -n "$srcdir" || local srcdir=`dirname "$0"`
+ #test -n "$srcdir" || local srcdir=.
eautoreconf --force --install --verbose "$srcdir"
}
@@ -43,11 +46,11 @@ src_configure(){
PYTHON_VERSION=3 econf ${myconf[@]}
}
-src_compile(){
- # build_boost.sh
- cd deps/boost || die
- ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
- ./b2 headers || die
- ./b2 install || die
- cd ../.. || die
-}
+#src_compile(){
+# # build_boost.sh
+# cd deps/boost || die
+# ./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
+# ./b2 headers --prefix=build || die
+# ./b2 install --prefix=build || die
+# cd ../.. || die
+#}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index d46f6d3e8..8fe79a34b 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -39,7 +39,7 @@ src_prepare(){
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-2.20/configure
+ use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.2.0/configure
PYTHON_VERSION=3 econf ${myconf[@]}
}
@@ -47,7 +47,8 @@ src_compile(){
# build_boost.sh
cd deps/boost || die
./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
- ./b2 headers || die
- ./b2 install || die
+ # https://github.com/TGAC/KAT/issues/92#issuecomment-383373418
+ ./b2 headers --ignore-site-config || die
+ ./b2 install --ignore-site-config || die
cd ../.. || die
}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/kat/files/, sci-biology/kat/
@ 2018-05-07 21:45 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2018-05-07 21:45 UTC (permalink / raw
To: gentoo-commits
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>
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2018-04-22 11:45 Martin Mokrejs
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