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commit: a3f4a06e9718b69c63c9fcf6a50e4268c26759dd |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Wed Apr 12 17:46:57 2017 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Apr 12 17:46:57 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3f4a06e |
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|
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sci-biology/nxtrim: drop patch accepted by upstream now |
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|
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Package-Manager: Portage-2.3.5, Repoman-2.3.2 |
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|
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sci-biology/nxtrim/files/Makefile.patch | 43 --------------------------------- |
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sci-biology/nxtrim/nxtrim-9999.ebuild | 5 ---- |
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2 files changed, 48 deletions(-) |
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|
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diff --git a/sci-biology/nxtrim/files/Makefile.patch b/sci-biology/nxtrim/files/Makefile.patch |
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deleted file mode 100644 |
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index fb7da0a50..000000000 |
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--- a/sci-biology/nxtrim/files/Makefile.patch |
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+++ /dev/null |
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@@ -1,43 +0,0 @@ |
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---- Makefile.ori 2017-04-06 23:38:08.591353594 +0200 |
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-+++ Makefile 2017-04-06 23:41:34.127107768 +0200 |
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-@@ -1,12 +1,12 @@ |
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--Cxx = g++ |
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-+CXX ?= g++ |
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- |
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- |
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--CFLAGS = -O3 |
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--LFLAGS= -lz |
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-+CXXFLAGS ?= -O3 |
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-+LFLAGS = -lz |
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- |
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- all: mergeReads nxtrim |
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- |
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--debug: CFLAGS = -Wall -g |
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-+debug: CXXFLAGS += -Wall -g |
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- debug: all |
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- |
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- GIT_HASH := $(shell git describe --abbrev=4 --always ) |
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-@@ -21,17 +21,17 @@ |
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- |
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- |
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- unit_test: test.cpp fastqlib.o utilityfunc.o matepair.o |
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-- $(CXX) $(CFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o unit_test $(LFLAGS) |
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-+ $(CXX) $(CXXFLAGS) test.cpp fastqlib.o utilityfunc.o matepair.o -o unit_test $(LFLAGS) |
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- nxtrim: nxtrim.cpp fastqlib.o utilityfunc.o matepair.o fastqlib.o version.h |
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-- $(CXX) $(CFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim $(LFLAGS) |
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-+ $(CXX) $(CXXFLAGS) nxtrim.cpp fastqlib.o utilityfunc.o matepair.o -o nxtrim $(LFLAGS) |
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- mergeReads: mergeReads.cpp fastqlib.o utilityfunc.o fastqlib.o githash.h version.h |
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-- $(CXX) $(CFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads $(LFLAGS) |
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-+ $(CXX) $(CXXFLAGS) mergeReads.cpp fastqlib.o utilityfunc.o -o mergeReads $(LFLAGS) |
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- matepair.o: matepair.cpp matepair.h fastqlib.h |
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-- $(CXX) $(CFLAGS) -c matepair.cpp |
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-+ $(CXX) $(CXXFLAGS) -c matepair.cpp |
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- fastqlib.o: fastqlib.cpp fastqlib.h utilityfunc.h |
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-- $(CXX) $(CFLAGS) -c fastqlib.cpp |
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-+ $(CXX) $(CXXFLAGS) -c fastqlib.cpp |
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- utilityfunc.o: utilityfunc.cpp utilityfunc.h |
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-- $(CXX) $(CFLAGS) -c utilityfunc.cpp |
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-+ $(CXX) $(CXXFLAGS) -c utilityfunc.cpp |
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- test: nxtrim |
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- bash example/run_test.sh |
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- clean: |
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|
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diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild |
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index 4eb879880..9a12a0226 100644 |
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--- a/sci-biology/nxtrim/nxtrim-9999.ebuild |
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+++ b/sci-biology/nxtrim/nxtrim-9999.ebuild |
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@@ -17,11 +17,6 @@ IUSE="" |
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DEPEND="" |
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RDEPEND="${DEPEND}" |
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|
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-src_prepare(){ |
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- eapply_user |
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- epatch "${FILESDIR}"/Makefile.patch # https://github.com/sequencing/NxTrim/pull/31 |
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-} |
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- |
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src_install(){ |
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dobin nxtrim mergeReads |
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dodoc README.md |
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