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