commit: bed71574b0b2911b0e667931508bb5b069883b64 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Apr 3 16:14:04 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Apr 3 16:14:40 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bed71574
sci-biology/cufflinks: Depend only on sci-biology/samtools:0.1-legacy Gentoo-Bug: 535716 * EAPI=6 * Updated boost in tree has fixed serialization for boost::shared_ptr * Build system is now orthogonal to sci-biology/samtools:0 and does not block updating to latest samtools Package-Manager: portage-2.2.28 sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 39 +++++++++++++++++++ .../files/cufflinks-2.2.1-samtools-legacy.patch | 44 ++++++++++++++++++++++ 2 files changed, 83 insertions(+) diff --git a/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild new file mode 100644 index 0000000..2ccac30 --- /dev/null +++ b/sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools flag-o-matic toolchain-funcs + +DESCRIPTION="Transcript assembly and differential expression/regulation for RNA-Seq" +HOMEPAGE="http://cufflinks.cbcb.umd.edu/"; +SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"; + +SLOT="0" +LICENSE="Artistic" +IUSE="debug" +KEYWORDS="~amd64 ~x86" + +DEPEND="sci-biology/samtools:0.1-legacy + >=dev-libs/boost-1.59.0:= + dev-cpp/eigen:3" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-samtools-legacy.patch + "${FILESDIR}"/${P}-flags.patch +) + +src_prepare() { + default + eautoreconf + append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3) +} + +src_configure() { + econf --disable-optim \ + --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \ + --with-bam="${EPREFIX}/usr/" \ + $(use_enable debug) +} diff --git a/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch new file mode 100644 index 0000000..374ce51 --- /dev/null +++ b/sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch @@ -0,0 +1,44 @@ +Modify the buildsystem to work with the legacy version of samtools, +which can coexist with the most recent version of samtools. +See also: https://bugs.gentoo.org/show_bug.cgi?id=577854 + +--- cufflinks-2.2.1/ax_bam.m4 ++++ cufflinks-2.2.1/ax_bam.m4 +@@ -102,7 +102,7 @@ + + AC_LANG_PUSH(C++) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ +- @%:@include <bam/bam.h> ++ @%:@include <bam-0.1-legacy/bam.h> + ]], [[ + ]])],[ + AC_MSG_RESULT(yes) +@@ -171,7 +171,7 @@ + + AC_LANG_PUSH(C++) + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[ +- @%:@include <bam/version.hpp> ++ @%:@include <bam-0.1-legacy/version.hpp> + ]], [[ + ]])],[ + AC_MSG_RESULT(yes) +@@ -189,7 +189,7 @@ + AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) + fi + else +- BAM_LIB="-lbam" ++ BAM_LIB="-lbam-0.1-legacy" + AC_SUBST(BAM_CPPFLAGS) + AC_SUBST(BAM_LDFLAGS) + AC_SUBST(BAM_LIB) +--- cufflinks-2.2.1/src/hits.h ++++ cufflinks-2.2.1/src/hits.h +@@ -18,7 +18,7 @@ + + #include <boost/shared_ptr.hpp> + +-#include <bam/sam.h> ++#include <bam-0.1-legacy/sam.h> + + #include "common.h" + #include "multireads.h"
