commit: dbff72983c149c6901adfa99351d1e0fa83e7bfe Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 30 17:17:50 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 30 17:17:50 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dbff7298
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 sci-biology/reapr/metadata.xml | 12 ++++++++ sci-biology/reapr/reapr-1.0.18.ebuild | 56 +++++++++++++++++++++++++++++++++++ 2 files changed, 68 insertions(+) diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</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 0000000..312219a --- /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" +}
