[gentoo-commits] proj/sci:master commit in: sci-biology/staden/files/, sci-biology/staden/

[Martin Mokrejs]

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"
+}