sci-biology/reapr: new package with bundled samtools, bamtools, tabix (nowadays part of samtools) and other binaries; does not link probably due to a clash of symbols with my system-wide installed -lbamtools

Package-Manager: portage-2.2.28

1 files changed, 56 insertions, 0 deletions

diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild
new file mode 100644
index 000000000..312219abb
--- /dev/null
+++ b/sci-biology/reapr/reapr-1.0.18.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
+	ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="" # does not link against -lbamtools
+IUSE=""
+
+# tested smalt versions 0.6.4 to 0.7.0.1 only
+DEPEND="sci-biology/bamtools
+	=sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18
+RDEPEND="${DEPEND}"
+#	sci-biology/smalt
+#	dev-perl/File-Basename
+#	dev-perl/File-Copy
+#	dev-perl/File-Spec
+#	perl-core/Getopt-Long
+#	dev-perl/List-Util
+#	dev-lang/R"
+
+S="${WORKDIR}"/Reapr_"${PV}"
+
+src_prepare(){
+	sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die
+	sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die
+	sed -e 's#-O3##' -i src/Makefile || die
+	sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die
+	#sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die
+	sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die
+	sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die
+}
+
+src_compile(){
+	cd third_party/tabix || die
+	emake # to yield tabix.o object
+	cd ../.. || die
+	cd src || die
+	emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a
+}
+
+src_install(){
+	dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf
+}
+
+pkg_postinst(){
+	einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"
+	einfo "You can view results with >=sci-biology/artemis*-15.0.0"
+}