* [gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/, sci-biology/nxtrim/files/
@ 2017-04-12 17:47 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2017-04-12 17:47 UTC (permalink / raw
To: gentoo-commits
commit: a3f4a06e9718b69c63c9fcf6a50e4268c26759dd
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr 12 17:46:57 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr 12 17:46:57 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3f4a06e
sci-biology/nxtrim: drop patch accepted by upstream now
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/nxtrim/files/Makefile.patch | 43 ---------------------------------
sci-biology/nxtrim/nxtrim-9999.ebuild | 5 ----
2 files changed, 48 deletions(-)
diff --git a/sci-biology/nxtrim/files/Makefile.patch b/sci-biology/nxtrim/files/Makefile.patch
deleted file mode 100644
index fb7da0a50..000000000
--- a/sci-biology/nxtrim/files/Makefile.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- 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) $(CXXFLAGS) -c utilityfunc.cpp
- test: nxtrim
- bash example/run_test.sh
- clean:
diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild
index 4eb879880..9a12a0226 100644
--- a/sci-biology/nxtrim/nxtrim-9999.ebuild
+++ b/sci-biology/nxtrim/nxtrim-9999.ebuild
@@ -17,11 +17,6 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}"
-src_prepare(){
- eapply_user
- epatch "${FILESDIR}"/Makefile.patch # https://github.com/sequencing/NxTrim/pull/31
-}
-
src_install(){
dobin nxtrim mergeReads
dodoc README.md
^ permalink raw reply related [flat|nested] 2+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/nxtrim/, sci-biology/nxtrim/files/
@ 2017-04-06 21:53 Martin Mokrejs
0 siblings, 0 replies; 2+ messages in thread
From: Martin Mokrejs @ 2017-04-06 21:53 UTC (permalink / raw
To: gentoo-commits
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) $(CXXFLAGS) -c utilityfunc.cpp
+ test: nxtrim
+ bash example/run_test.sh
+ clean:
diff --git a/sci-biology/nxtrim/metadata.xml b/sci-biology/nxtrim/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/nxtrim/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild
new file mode 100644
index 000000000..856f63662
--- /dev/null
+++ b/sci-biology/nxtrim/nxtrim-9999.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit git-r3 eutils
+
+DESCRIPTION="Trim Illumina TruSeq adapters and split reads by NEBnext MatePair linker"
+HOMEPAGE="https://github.com/sequencing/NxTrim"
+EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ eapply_user
+ epatch "${FILESDIR}"/Makefile.patch # https://github.com/sequencing/NxTrim/pull/31
+}
+
+src_install(){
+ dobin nxtrim mergeReads
+ dodoc README.md
+}
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