commit: eacdfe16dd975d80b8d261c56f20c5843299651b Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Wed Mar 8 21:35:39 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Wed Mar 8 22:16:14 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eacdfe16
sci-biology/blat: Modernise to EAPI 6 Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165 sci-biology/blat/blat-34-r2.ebuild | 42 +++++ .../blat/files/blat-34-fix-build-system.patch | 207 +++++++++++++++++++++ 2 files changed, 249 insertions(+) diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild new file mode 100644 index 00000000000..e10bc367a31 --- /dev/null +++ b/sci-biology/blat/blat-34-r2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_PN=${PN}Src + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/"; +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"; + +LICENSE="blat" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="" +DEPEND="app-arch/unzip" + +S=${WORKDIR}/${MY_PN} + +PATCHES=( "${FILESDIR}"/${PN}-34-fix-build-system.patch ) + +src_compile() { + tc-export AR CC + + export HOME="${S}" + export MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + + mkdir -p bin/${MACHTYPE} || die + default +} + +src_install() { + export MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + + dobin bin/${MACHTYPE}/* +} diff --git a/sci-biology/blat/files/blat-34-fix-build-system.patch b/sci-biology/blat/files/blat-34-fix-build-system.patch new file mode 100644 index 00000000000..361149cc121 --- /dev/null +++ b/sci-biology/blat/files/blat-34-fix-build-system.patch @@ -0,0 +1,207 @@ +--- a/blat/makefile ++++ b/blat/makefile +@@ -7,7 +7,7 @@ + O = blat.o + + blat: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/blat $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/blat${EXE} + + all: +--- a/gfClient/makefile ++++ b/gfClient/makefile +@@ -8,5 +8,5 @@ + X = gfClient + + gfClient: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} +--- a/gfServer/makefile ++++ b/gfServer/makefile +@@ -8,7 +8,7 @@ + X = gfServer + + gfServer: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/$X $O $(MYLIBS) $L + ${STRIP} ${BINDIR}/$X${EXE} + + test: +--- a/hg/pslPretty/makefile ++++ b/hg/pslPretty/makefile +@@ -8,7 +8,7 @@ + O = pslPretty.o + + pslPretty: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslPretty $O $(MYLIBS) $L + + test:: testRna testDnax + +--- a/hg/pslReps/makefile ++++ b/hg/pslReps/makefile +@@ -9,7 +9,7 @@ + O = pslReps.o + + pslReps: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L + + lib: + cd ../../lib && ${MAKE} +--- a/hg/pslSort/makefile ++++ b/hg/pslSort/makefile +@@ -8,7 +8,7 @@ + O = pslSort.o + + pslSort: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L + + + lib: +--- a/inc/common.mk ++++ b/inc/common.mk +@@ -1,20 +1,15 @@ +-CC=gcc +-ifeq (${COPT},) +- COPT=-O +-endif +-CFLAGS= + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} + HG_WARN=-Wformat -Wimplicit -Wuninitialized -Wreturn-type + HG_INC=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc + + # Stronger warning checks, and warnings-->errors, for libraries and CGIs: + ifeq (darwin,$(findstring darwin,${OSTYPE})) +- HG_WARN_ERR = -DJK_WARN -Wall -Werror -Wno-unused-variable ++ HG_WARN_ERR = -DJK_WARN -Wall -Wno-unused-variable + else + ifeq (solaris,$(findstring solaris,${OSTYPE})) + HG_WARN_ERR = -DJK_WARN -Wall + else +- HG_WARN_ERR = -DJK_WARN -Wall -Werror ++ HG_WARN_ERR = -DJK_WARN -Wall + endif + endif + # Apply the stronger checks to all code on our development machine: +@@ -37,7 +32,7 @@ + endif + MKDIR=mkdir -p + ifeq (${STRIP},) +- STRIP=strip ++ STRIP=true + endif + CVS=cvs + +--- a/jkOwnLib/makefile ++++ b/jkOwnLib/makefile +@@ -9,7 +9,7 @@ + T = ../lib/$(MACHTYPE)/jkOwnLib.a + + $(T): $(O) ../lib/$(MACHTYPE) +- ar rcus $(T) $(O) ++ $(AR) rcus $(T) $(O) + + ../lib/$(MACHTYPE): + mkdir ../lib/$(MACHTYPE) +--- a/lib/makefile ++++ b/lib/makefile +@@ -32,7 +32,7 @@ + + + $(MACHTYPE)/jkweb.a: $(O) $(MACHTYPE) +- ar rcus $(MACHTYPE)/jkweb.a $(O) ++ $(AR) rcus $(MACHTYPE)/jkweb.a $(O) + + $(MACHTYPE): + mkdir $(MACHTYPE) +--- a/makefile ++++ b/makefile +@@ -1,18 +1,18 @@ + all: +- cd lib && ${MAKE} +- cd jkOwnLib && ${MAKE} +- cd blat && $(MAKE) +- cd gfClient && $(MAKE) +- cd gfServer && $(MAKE) +- cd hg/pslPretty && $(MAKE) +- cd hg/pslReps && $(MAKE) +- cd hg/pslSort && $(MAKE) +- cd utils/nibFrag && $(MAKE) +- cd utils/faToNib && $(MAKE) +- cd utils/faToTwoBit && $(MAKE) +- cd utils/twoBitToFa && $(MAKE) +- cd utils/twoBitInfo && $(MAKE) +- cd webBlat && $(MAKE) ++ $(MAKE) -C lib ++ $(MAKE) -C jkOwnLib ++ $(MAKE) -C blat ++ $(MAKE) -C gfClient ++ $(MAKE) -C gfServer ++ $(MAKE) -C hg/pslPretty ++ $(MAKE) -C hg/pslReps ++ $(MAKE) -C hg/pslSort ++ $(MAKE) -C utils/nibFrag ++ $(MAKE) -C utils/faToNib ++ $(MAKE) -C utils/faToTwoBit ++ $(MAKE) -C utils/twoBitToFa ++ $(MAKE) -C utils/twoBitInfo ++ $(MAKE) -C webBlat + + clean: + rm -f */*.o */*/*.o +--- a/utils/faToNib/makefile ++++ b/utils/faToNib/makefile +@@ -8,4 +8,4 @@ + O = faToNib.o + + faToNib: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/faToNib $O $(MYLIBS) $L +--- a/utils/faToTwoBit/makefile ++++ b/utils/faToTwoBit/makefile +@@ -7,7 +7,7 @@ + O = faToTwoBit.o + + faToTwoBit: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/faToTwoBit $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/faToTwoBit${EXE} + + clean: +--- a/utils/nibFrag/makefile ++++ b/utils/nibFrag/makefile +@@ -4,7 +4,7 @@ + O = nibFrag.o + + nibFrag: $(O) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/nibFrag $O ../../lib/$(MACHTYPE)/jkweb.a + + + +--- a/utils/twoBitInfo/makefile ++++ b/utils/twoBitInfo/makefile +@@ -7,7 +7,7 @@ + O = twoBitInfo.o + + twoBitInfo: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitInfo $O ${MYLIBS} $L + ${STRIP} ${BINDIR}/twoBitInfo${EXE} + + clean: +--- a/utils/twoBitToFa/makefile ++++ b/utils/twoBitToFa/makefile +@@ -8,7 +8,7 @@ + O = twoBitToFa.o + + twoBitToFa: $O ${MYLIBS} +- ${CC} ${COPT} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L ++ ${CC} ${COPT} ${LDFLAGS} -o ${BINDIR}/twoBitToFa $O ${MYLIBS} $L + #${STRIP} ${BINDIR}/twoBitToFa${EXE} + + clean:
