sci-biology/nxtrim: new package

Package-Manager: Portage-2.3.5, Repoman-2.3.1

3 files changed, 83 insertions, 0 deletions

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) $(CXXFLAGS) -c utilityfunc.cpp
+ test: nxtrim
+ 	bash example/run_test.sh
+ clean:
diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/nxtrim/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild
new file mode 100644
index 000000000..856f63662
--- /dev/null
+++ b/sci-biology/nxtrim/nxtrim-9999.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit git-r3 eutils
+
+DESCRIPTION="Trim Illumina TruSeq adapters and split reads by NEBnext MatePair linker"
+HOMEPAGE="https://github.com/sequencing/NxTrim"
+EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	eapply_user
+	epatch "${FILESDIR}"/Makefile.patch # https://github.com/sequencing/NxTrim/pull/31
+}
+
+src_install(){
+	dobin nxtrim mergeReads
+	dodoc README.md
+}