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
}
