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
