commit: e459544d4d91e198e5c5e386a2052dc2600e1286 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 22 18:11:45 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 22 18:11:45 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e459544d
sci-biology/kat: improve -8888 ebuild Try call setup.py on our own so that it could receive ${DESTDIR} contents. This still does not work. The ebuild drops bundled boost copy but retains bundled seqan headers and the modified copy of jellyfish. They won't interfere with with site-wide installed packages of those tools in Gentoo. The modified jellyfish is linked-in statically and binaries have 'kat_' prefix. The kat-2.4.1.ebuild and -9999.ebuild should later get same logic like appears in -8888.ebuild. Currently they stick to upstream's approach of using bundled boost too. All ebuilds suffer same problem: the python files do not get installed at all. Package-Manager: Portage-2.3.28, Repoman-2.3.9 .../kat/files/kat-2.4.1-do-not-run-setup.py.patch | 30 ++++ .../kat/files/kat-2.4.1-ignore-bundled-deps.patch | 127 +++++++--------- .../kat/files/kat-2.4.1-rename-jellyfish.patch | 159 --------------------- sci-biology/kat/kat-2.4.1.ebuild | 12 +- sci-biology/kat/kat-8888.ebuild | 50 +++++-- sci-biology/kat/metadata.xml | 4 + 6 files changed, 132 insertions(+), 250 deletions(-) diff --git a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch new file mode 100644 index 000000000..a00c971a6 --- /dev/null +++ b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch @@ -0,0 +1,30 @@ +--- scripts/Makefile.am.ori 2018-04-22 16:02:12.829046527 +0200 ++++ scripts/Makefile.am 2018-04-22 16:05:31.444532061 +0200 +@@ -1,27 +1,6 @@ + AUTOMAKE_OPTIONS = subdir-objects + + +-if MAKE_PYKAT_INSTALL +- +-install-exec-hook: +- export PYTHONPATH=$(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 index d1816498e..649f3ecd8 100644 --- 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 @@ -6,51 +6,56 @@ 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_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 ${PYTHON_VERSION}. Plotting and downstream analysis enabled." ---- Makefile.am.ori 2018-04-22 12:23:58.756197763 +0200 -+++ Makefile.am 2018-04-22 12:24:21.176832618 +0200 -@@ -19,7 +19,7 @@ - dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh +--- lib/Makefile.am.ori 2018-04-22 15:30:34.983653065 +0200 ++++ lib/Makefile.am 2018-04-22 15:30:46.143961300 +0200 +@@ -7,8 +7,7 @@ - # SRC DIRS --make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests -+make_dirs=lib src tests + libkat_la_LDFLAGS = \ + -version-info 2:4:0 \ +- -L../deps/jellyfish-2.2.0 \ +- -L../deps/boost/build/lib ++ -L../deps/jellyfish-2.2.0 - if MAKE_PYKAT - make_dirs += scripts ---- tests/Makefile.am.ori 2018-04-22 12:31:02.738203085 +0200 -+++ tests/Makefile.am 2018-04-22 12:34:15.043648336 +0200 -@@ -29,8 +29,7 @@ + libkat_la_SOURCES = \ + src/matrix_metadata_extractor.cc \ +@@ -31,7 +30,6 @@ - AM_CPPFLAGS = \ + libkat_la_CPPFLAGS = \ + -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ +- -I$(top_srcdir)/deps/boost/build/include \ -I$(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$(PYTHON_VERSION)/site-packages"' \ -@@ -60,7 +59,6 @@ + @AM_CPPFLAGS@ +--- src/Makefile.am.ori 2018-04-22 15:30:46.203962959 +0200 ++++ src/Makefile.am 2018-04-22 15:31:41.385487008 +0200 +@@ -14,7 +14,6 @@ + kat_CPPFLAGS = \ + -I$(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$(PYTHON_VERSION)/site-packages"' \ + @AM_CPPFLAGS@ +@@ -23,17 +22,16 @@ -static \ - -L. \ -L../lib \ -- -L../deps/jellyfish-2.2.0 \ - -L../deps/boost/build/lib \ + -L../deps/jellyfish-2.2.0 \ +- -L../deps/boost/build/lib \ @AM_LDFLAGS@ -@@ -69,11 +67,11 @@ - -lgtest \ + kat_LDADD = \ -lkat \ -lkat_jellyfish \ - ../deps/boost/build/lib/libboost_timer.a \ -- ../deps/boost/build/lib/libboost_chrono.a \ -- ../deps/boost/build/lib/libboost_filesystem.a \ -- ../deps/boost/build/lib/libboost_program_options.a \ -- ../deps/boost/build/lib/libboost_system.a \ +- ../deps/boost/build/lib/libboost_chrono.a \ +- ../deps/boost/build/lib/libboost_filesystem.a \ +- ../deps/boost/build/lib/libboost_program_options.a \ +- ../deps/boost/build/lib/libboost_system.a \ + -lboost_timer \ + -lboost_chrono \ + -lboost_filesystem \ @@ -58,36 +63,34 @@ + -lboost_system \ @AM_LIBS@ - include gtest.mk ---- src/Makefile.am.ori 2018-04-22 12:34:41.874408065 +0200 -+++ src/Makefile.am 2018-04-22 12:36:33.567570728 +0200 -@@ -12,9 +12,7 @@ - @AM_CXXFLAGS@ - - kat_CPPFLAGS = \ -- -I$(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 \ + 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@ -@@ -22,18 +20,16 @@ - kat_LDFLAGS = \ - -static \ +@@ -61,7 +60,6 @@ + -L. \ -L../lib \ -- -L../deps/jellyfish-2.2.0 \ + -L../deps/jellyfish-2.2.0 \ - -L../deps/boost/build/lib \ @AM_LDFLAGS@ - kat_LDADD = \ + 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 \ +- ../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 \ @@ -95,26 +98,4 @@ + -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@ + include gtest.mk 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 deleted file mode 100644 index 81d4f7d18..000000000 --- a/sci-biology/kat/files/kat-2.4.1-rename-jellyfish.patch +++ /dev/null @@ -1,159 +0,0 @@ ---- 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 f1635e9e8..29f11c9f6 100644 --- a/sci-biology/kat/kat-2.4.1.ebuild +++ b/sci-biology/kat/kat-2.4.1.ebuild @@ -18,12 +18,12 @@ KEYWORDS="" IUSE="cpu_flags_x86_sse doc" DEPEND=" - >=dev-libs/boost-1.52 - dev-python/tabulate - dev-python/matplotlib - dev-python/numpy - sci-libs/scipy - doc? ( dev-python/sphinx )" + >=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}] )" RDEPEND="${DEPEND}" # contains bundled *modified* version of jellyfish-2.2 which should install under different filenames # contains embedded sci-biology/seqan diff --git a/sci-biology/kat/kat-8888.ebuild b/sci-biology/kat/kat-8888.ebuild index 2c88b2a25..a8a776c29 100644 --- a/sci-biology/kat/kat-8888.ebuild +++ b/sci-biology/kat/kat-8888.ebuild @@ -6,7 +6,7 @@ EAPI=6 PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5 # https://github.com/Ensembl/Bio-DB-HTS/issues/30 -inherit git-r3 eutils flag-o-matic autotools +inherit git-r3 eutils flag-o-matic autotools distutils-r1 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" HOMEPAGE="https://github.com/TGAC/KAT" @@ -15,30 +15,56 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git" LICENSE="GPL-3+" SLOT="0" KEYWORDS="" -IUSE="cpu_flags_x86_sse doc" +IUSE="cpu_flags_x86_sse doc tex" DEPEND=" - >=dev-libs/boost-1.52 - dev-python/tabulate - dev-python/matplotlib - dev-python/numpy - sci-libs/scipy - doc? ( dev-python/sphinx )" + >=dev-libs/boost-1.52[${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[${PYTHON_USEDEP}] ) + tex? ( dev-tex/latexmk )" RDEPEND="${DEPEND}" # contains bundled a *modified* version of jellyfish-2.2.0 (libkat_jellyfish.{a,so}) # contains embedded sci-biology/seqan src_prepare(){ default - rm -rf deps || die "Failed to zap bundled seqan-library-2.0.0 jellyfish-2.2.0 boost" + # 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-rename-jellyfish.patch - eautoreconf --force --install --verbose "$srcdir" + epatch "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch + eautoreconf } 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 - PYTHON_VERSION=3 econf ${myconf[@]} + econf ${myconf[@]} +} + +src_compile(){ + emake + cd doc && make latexpdf || die +} + +src_install(){ + # emake install + default + # install python files (the "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch + # removed code which ignored ${DESTDIR}) + # https://github.com/TGAC/KAT/issues/94#issuecomment-383385701 + cd scripts || die + esetup.py install --record install_files.txt +} + +# probably the below is not needed (does not seem to work) +python_install_all() { + cd scripts || die + distutils-r1_python_install_all } diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml index 6810aabae..eb95c0c06 100644 --- a/sci-biology/kat/metadata.xml +++ b/sci-biology/kat/metadata.xml @@ -12,4 +12,8 @@ <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>