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From: "David Seifert" <soap@gentoo.org>
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Message-ID: <1459700080.bed71574b0b2911b0e667931508bb5b069883b64.soap@gentoo>
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/cufflinks/files/, sci-biology/cufflinks/
X-VCS-Repository: repo/gentoo
X-VCS-Files: sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild sci-biology/cufflinks/files/cufflinks-2.2.1-samtools-legacy.patch
X-VCS-Directories: sci-biology/cufflinks/files/ sci-biology/cufflinks/
X-VCS-Committer: soap
X-VCS-Committer-Name: David Seifert
X-VCS-Revision: bed71574b0b2911b0e667931508bb5b069883b64
X-VCS-Branch: master
Date: Sun, 3 Apr 2016 16:14:47 +0000 (UTC)
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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"