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

2 files changed, 83 insertions, 0 deletions

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 000000000000..2ccac3099b0d
--- /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 000000000000..374ce519ef86
--- /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"