commit: 77bec8065ed5b62840430e4d0e90814616757a6f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Apr 6 21:53:28 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 6 21:53:28 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=77bec806
sci-biology/nxtrim: new package Package-Manager: Portage-2.3.5, Repoman-2.3.1 sci-biology/nxtrim/files/Makefile.patch | 43 +++++++++++++++++++++++++++++++++ sci-biology/nxtrim/metadata.xml | 12 +++++++++ sci-biology/nxtrim/nxtrim-9999.ebuild | 28 +++++++++++++++++++++ 3 files changed, 83 insertions(+) diff --git a/sci-biology/nxtrim/files/Makefile.patch b/sci-biology/nxtrim/files/Makefile.patch new file mode 100644 index 000000000..fb7da0a50 --- /dev/null +++ b/sci-biology/nxtrim/files/Makefile.patch @@ -0,0 +1,43 @@ +--- Makefile.ori 2017-04-06 23:38:08.591353594 +0200 ++++ Makefile 2017-04-06 23:41:34.127107768 +0200 +@@ -1,12 +1,12 @@ +-Cxx = g++ ++CXX ?= g++ + + +-CFLAGS = -O3 +-LFLAGS= -lz ++CXXFLAGS ?= -O3 ++LFLAGS = -lz + + all: mergeReads nxtrim + +-debug: CFLAGS = -Wall -g ++debug: CXXFLAGS += -Wall -g + debug: all + + GIT_HASH := $(shell git describe --abbrev=4 --always ) +@@ -21,17 +21,17 @@ + + + unit_test: test.cpp fastqlib.o utilityfunc.o matepair.o +- $(CXX) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o unit_test $(LFLAGS) ++ $(CXX) $(CXXFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o unit_test $(LFLAGS) + nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o version.h +- $(CXX) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim $(LFLAGS) ++ $(CXX) $(CXXFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim $(LFLAGS) + mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h version.h +- $(CXX) $(CFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads $(LFLAGS) ++ $(CXX) $(CXXFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads $(LFLAGS) + matepair.o: matepair.cpp matepair.h fastqlib.h +- $(CXX) $(CFLAGS) -c matepair.cpp ++ $(CXX) $(CXXFLAGS) -c matepair.cpp + fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h +- $(CXX) $(CFLAGS) -c fastqlib.cpp ++ $(CXX) $(CXXFLAGS) -c fastqlib.cpp + utilityfunc.o: utilityfunc.cpp utilityfunc.h +- $(CXX) $(CFLAGS) -c utilityfunc.cpp ++ $(CXX) $(CXXFLAGS) -c utilityfunc.cpp + test: nxtrim + bash example/run_test.sh + clean: diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/nxtrim/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild new file mode 100644 index 000000000..856f63662 --- /dev/null +++ b/sci-biology/nxtrim/nxtrim-9999.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit git-r3 eutils + +DESCRIPTION="Trim Illumina TruSeq adapters and split reads by NEBnext MatePair linker" +HOMEPAGE="https://github.com/sequencing/NxTrim"; +EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git"; + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + eapply_user + epatch "${FILESDIR}"/Makefile.patch # https://github.com/sequencing/NxTrim/pull/31 +} + +src_install(){ + dobin nxtrim mergeReads + dodoc README.md +}
