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commit: dbff72983c149c6901adfa99351d1e0fa83e7bfe |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Wed Mar 30 17:17:50 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Mar 30 17:17:50 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dbff7298 |
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|
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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 |
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|
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Package-Manager: portage-2.2.28 |
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|
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sci-biology/reapr/metadata.xml | 12 ++++++++ |
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sci-biology/reapr/reapr-1.0.18.ebuild | 56 +++++++++++++++++++++++++++++++++++ |
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2 files changed, 68 insertions(+) |
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|
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diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml |
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new file mode 100644 |
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index 0000000..f68a1b6 |
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--- /dev/null |
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+++ b/sci-biology/reapr/metadata.xml |
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@@ -0,0 +1,12 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <maintainer type="person"> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+</pkgmetadata> |
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|
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diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild |
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new file mode 100644 |
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index 0000000..312219a |
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--- /dev/null |
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+++ b/sci-biology/reapr/reapr-1.0.18.ebuild |
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@@ -0,0 +1,56 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=5 |
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+ |
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+DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads" |
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+HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr" |
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+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz |
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+ ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf" |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+KEYWORDS="" # does not link against -lbamtools |
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+IUSE="" |
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+ |
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+# tested smalt versions 0.6.4 to 0.7.0.1 only |
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+DEPEND="sci-biology/bamtools |
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+ =sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18 |
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+RDEPEND="${DEPEND}" |
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+# sci-biology/smalt |
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+# dev-perl/File-Basename |
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+# dev-perl/File-Copy |
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+# dev-perl/File-Spec |
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+# perl-core/Getopt-Long |
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+# dev-perl/List-Util |
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+# dev-lang/R" |
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+ |
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+S="${WORKDIR}"/Reapr_"${PV}" |
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+ |
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+src_prepare(){ |
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+ sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die |
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+ sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die |
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+ sed -e 's#-O3##' -i src/Makefile || die |
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+ sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die |
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+ #sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die |
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+ sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die |
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+ sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die |
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+} |
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+ |
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+src_compile(){ |
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+ cd third_party/tabix || die |
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+ emake # to yield tabix.o object |
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+ cd ../.. || die |
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+ cd src || die |
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+ emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a |
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+} |
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+ |
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+src_install(){ |
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+ dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf |
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+} |
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+ |
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+pkg_postinst(){ |
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+ einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz" |
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+ einfo "You can view results with >=sci-biology/artemis*-15.0.0" |
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+} |