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

3 files changed, 70 insertions, 0 deletions

diff --git a/sci-biology/reapr/Manifest b/sci-biology/reapr/Manifest
new file mode 100644
index 000000000..bca2dc435
--- /dev/null
+++ b/sci-biology/reapr/Manifest
@@ -0,0 +1,2 @@
+DIST Reapr_1.0.18.manual.pdf 325751 SHA256 304b7b7b725abc285791d8be3b2aaf6f4afeb38852ce91fa5635dc0a9913a517 SHA512 2960d93a330bd6a0aeda749213a83dc4fcbc5128be9c6bd1917ec2abea2def9406bbedad764d48d83b7f95c2da6207a027f98b341299d85c6ed898c5ca7b370f WHIRLPOOL 39744ee90218bdcad6fc630303a9453517d7fd0ecddb357cb354ee192c32d984af0b3cb1449165ef0d81e12ef87448d4e329fd29e4264594ff15f00d2fa19482
+DIST Reapr_1.0.18.tar.gz 7966110 SHA256 6d691b5b49c58aef332e771d339e32097a7696e9c68bd8f16808b46d648b6660 SHA512 12f1e97da6b6a3d080df29d9055aaf4ab2d02eb19a6c9eecb9d1e7268bf13bbe531feda6496d4b74c63ab53db0d1be15ed72f3391c47f9b1a23c34ed6a6c5fcb WHIRLPOOL 2d8079e123785f0984f1d6c8188c7c477a6d49a8f0632e430cb4865602e5a160b8d03b5e4c9ede4653c3a88d9296261f4356ee5423d572fda7cc0218564416d6
diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/reapr/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
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"
+}