commit: 87faa2f0b78c074a433f5ff20612b34b7b8c4557 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jul 31 20:36:50 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jul 31 20:36:50 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87faa2f0
sci-biology/staden: version bump, beta10-zlib.patch patch not needed now Package-Manager: portage-2.3.0 .../staden/files/staden-2.0.0_beta11-ldflags.patch | 30 ++++++++ sci-biology/staden/staden-2.0.0_beta11.ebuild | 83 ++++++++++++++++++++++ 2 files changed, 113 insertions(+) diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch new file mode 100644 index 0000000..735feb3 --- /dev/null +++ b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch @@ -0,0 +1,30 @@ + abi/Makefile | 2 +- + alf/Makefile | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/abi/Makefile b/abi/Makefile +index 3c1f8fb..58b4353 100644 +--- a/abi/Makefile ++++ b/abi/Makefile +@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN) + $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC) + + getABIdate: $(OBJSD) +- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) ++ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) + + getABIcomment: $(OBJSC) + $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC) +diff --git a/alf/Makefile b/alf/Makefile +index 94b7480..ef41a26 100644 +--- a/alf/Makefile ++++ b/alf/Makefile +@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC) + ALFOBJ = alfsplit.o + + alfsplit: $(ALFOBJ) +- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) ++ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) + + RSOBJ = $(ALFBIN)/2rs.o + diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild new file mode 100644 index 0000000..8094672 --- /dev/null +++ b/sci-biology/staden/staden-2.0.0_beta11.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes + +inherit autotools-utils eutils flag-o-matic fortran-2 multilib + +DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" +HOMEPAGE="http://sourceforge.net/projects/staden"; +SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" + +LICENSE="staden" +SLOT="0" +KEYWORDS="" +IUSE="debug doc fortran png tcl tk X zlib" + +# either g77 or gfortran must be available +# edit src/mk/linux.mk accordingly +# +# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 +# +# +# + +DEPEND=" + app-arch/xz-utils + dev-lang/tk:0= + dev-tcltk/tklib + media-libs/libpng:0 + sci-biology/samtools:0 + >=sci-libs/io_lib-1.13.8 + sys-libs/zlib" +RDEPEND="${DEPEND} + >=dev-tcltk/iwidgets-4.0 + tcl? ( >=dev-tcltk/itcl-3.2 ) + tk? ( >=dev-tcltk/itk-3.2 ) + net-misc/curl + doc? ( sci-biology/staden_doc )" + +S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=("${FILESDIR}"/${P}-ldflags.patch) + +src_prepare() { + sed \ + -e 's:svnversion:false:' \ + -i configure.in || die + + AT_M4DIR=ac_stubs autotools-utils_src_prepare +} + +src_configure(){ + local myeconfargs=() + use X && myeconfargs+=( --with-x ) + myeconfargs+=( + --with-tklib=/usr/$(get_libdir)/tklib + ) + use amd64 && myeconfargs+=( --enable-64bit ) + use debug && append-cflags "-DCACHE_REF_DEBUG" + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + # install the LDPATH so that it appears in /etc/ld.so.conf after env-update + # subsequently, apps linked against /usr/lib/staden can be run because + # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' + # somehow for gap2caf, for example + cat >> "${T}"/99staden <<- EOF + STADENROOT="${EPREFIX}"/usr/share/staden + LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" + EOF + doenvd "${T}"/99staden +} + +pkg_postinst(){ + einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"; +}
