From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-biology/blat/Manifest | 1 + sci-biology/blat/blat-34-r1.ebuild | 45 +++++++ sci-biology/blat/blat-34.ebuild | 34 +++++ sci-biology/blat/files/34-gentoo.patch | 226 +++++++++++++++++++++++++++++++++ sci-biology/blat/metadata.xml | 5 + 5 files changed, 311 insertions(+) create mode 100644 sci-biology/blat/Manifest create mode 100644 sci-biology/blat/blat-34-r1.ebuild create mode 100644 sci-biology/blat/blat-34.ebuild create mode 100644 sci-biology/blat/files/34-gentoo.patch create mode 100644 sci-biology/blat/metadata.xml (limited to 'sci-biology/blat') diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest new file mode 100644 index 000000000000..c1b249e1a095 --- /dev/null +++ b/sci-biology/blat/Manifest @@ -0,0 +1 @@ +DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild new file mode 100644 index 000000000000..c61327420f26 --- /dev/null +++ b/sci-biology/blat/blat-34-r1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=4 + +inherit eutils 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}${PV}.zip" + +SLOT="0" +LICENSE="blat" +KEYWORDS="~amd64 ~x86 ~x64-macos" +IUSE="" + +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + sed \ + -e "1i\CFLAGS=${CFLAGS}" \ + -e "1i\LDFLAGS=${LDFLAGS}" \ + -i inc/common.mk || die + tc-export CC +} + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + mkdir -p "${S}/bin/${MACHTYPE}" + emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild new file mode 100644 index 000000000000..41d48bf26bd3 --- /dev/null +++ b/sci-biology/blat/blat-34.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +inherit toolchain-funcs + +DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" +LICENSE="blat" +HOMEPAGE="http://www.cse.ucsc.edu/~kent/" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +MY_PN="${PN}Src" +SRC_URI="http://www.soe.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" +S="${WORKDIR}/${MY_PN}" + +DEPEND="app-arch/unzip" +RDEPEND="" + +src_compile() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + sed -i 's/-Werror//; s/CFLAGS=//;' "${S}/inc/common.mk" + sed -i 's/\(${STRIP} \)/#\1/' "${S}"/{*/makefile,utils/*/makefile,*/*.mk} + mkdir -p "${S}/bin/${MACHTYPE}" + emake MACHTYPE="${MACHTYPE}" HOME="${S}" || die "emake failed" +} + +src_install() { + MACHTYPE=$(tc-arch) + [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" + dobin "${S}/bin/${MACHTYPE}/"* +} diff --git a/sci-biology/blat/files/34-gentoo.patch b/sci-biology/blat/files/34-gentoo.patch new file mode 100644 index 000000000000..8bdd05bff68d --- /dev/null +++ b/sci-biology/blat/files/34-gentoo.patch @@ -0,0 +1,226 @@ + blat/makefile | 2 +- + gfClient/makefile | 2 +- + gfServer/makefile | 2 +- + hg/pslPretty/makefile | 2 +- + hg/pslReps/makefile | 2 +- + hg/pslSort/makefile | 2 +- + inc/common.mk | 11 +++-------- + makefile | 28 ++++++++++++++-------------- + utils/faToNib/makefile | 2 +- + utils/faToTwoBit/makefile | 2 +- + utils/nibFrag/makefile | 2 +- + utils/twoBitInfo/makefile | 2 +- + utils/twoBitToFa/makefile | 2 +- + 13 files changed, 28 insertions(+), 33 deletions(-) + +diff --git a/blat/makefile b/blat/makefile +index b889c7b..739503a 100644 +--- a/blat/makefile ++++ b/blat/makefile +@@ -7,7 +7,7 @@ MYLIBS = $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a + 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: +diff --git a/gfClient/makefile b/gfClient/makefile +index c3288de..36e957e 100644 +--- a/gfClient/makefile ++++ b/gfClient/makefile +@@ -8,5 +8,5 @@ O = gfClient.o + 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} +diff --git a/gfServer/makefile b/gfServer/makefile +index c06b3a5..f042d22 100644 +--- a/gfServer/makefile ++++ b/gfServer/makefile +@@ -8,7 +8,7 @@ O = gfServer.o + 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: +diff --git a/hg/pslPretty/makefile b/hg/pslPretty/makefile +index c780b96..cbbcd0d 100644 +--- a/hg/pslPretty/makefile ++++ b/hg/pslPretty/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + 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 + +diff --git a/hg/pslReps/makefile b/hg/pslReps/makefile +index 6e8f6d7..2b73b60 100644 +--- a/hg/pslReps/makefile ++++ b/hg/pslReps/makefile +@@ -9,7 +9,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + 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} +diff --git a/hg/pslSort/makefile b/hg/pslSort/makefile +index 81fe083..eb63257 100644 +--- a/hg/pslSort/makefile ++++ b/hg/pslSort/makefile +@@ -8,7 +8,7 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + O = pslSort.o + + pslSort: $O $(MYLIBS) +- ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L ++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${BINDIR}/pslSort $O $(MYLIBS) $L + + + lib: +diff --git a/inc/common.mk b/inc/common.mk +index 1823163..3a04e2b 100644 +--- a/inc/common.mk ++++ b/inc/common.mk +@@ -1,20 +1,15 @@ +-CC=gcc +-ifeq (${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,${OSTYPE})) + HG_WARN_ERR = -DJK_WARN -Wall + else +- HG_WARN_ERR = -DJK_WARN -Wall -Werror ++ HG_WARN_ERR = -DJK_WARN -Wall + endif + endif + # Apply the stronger checks to all code on our development machine: +@@ -37,7 +32,7 @@ ifeq (${BINDIR},) + endif + MKDIR=mkdir -p + ifeq (${STRIP},) +- STRIP=strip ++ STRIP=true + endif + CVS=cvs + +diff --git a/makefile b/makefile +index 6f9fddf..dded1cd 100644 +--- 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 +diff --git a/utils/faToNib/makefile b/utils/faToNib/makefile +index fd0e3eb..63a1593 100644 +--- a/utils/faToNib/makefile ++++ b/utils/faToNib/makefile +@@ -8,4 +8,4 @@ MYLIBS = $(MYLIBDIR)/jkweb.a + 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 +diff --git a/utils/faToTwoBit/makefile b/utils/faToTwoBit/makefile +index b1b44a9..1e8c1c8 100644 +--- a/utils/faToTwoBit/makefile ++++ b/utils/faToTwoBit/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + 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: +diff --git a/utils/nibFrag/makefile b/utils/nibFrag/makefile +index 260a6f3..e37b9ab 100755 +--- a/utils/nibFrag/makefile ++++ b/utils/nibFrag/makefile +@@ -4,7 +4,7 @@ include ../../inc/common.mk + 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 + + + +diff --git a/utils/twoBitInfo/makefile b/utils/twoBitInfo/makefile +index 649784f..9434d1c 100644 +--- a/utils/twoBitInfo/makefile ++++ b/utils/twoBitInfo/makefile +@@ -7,7 +7,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + 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: +diff --git a/utils/twoBitToFa/makefile b/utils/twoBitToFa/makefile +index cf979f2..081f3b8 100644 +--- a/utils/twoBitToFa/makefile ++++ b/utils/twoBitToFa/makefile +@@ -8,7 +8,7 @@ MYLIBS = ${MYLIBDIR}/jkweb.a + 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: diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml new file mode 100644 index 000000000000..f17a827e3101 --- /dev/null +++ b/sci-biology/blat/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology + -- cgit v1.2.3-65-gdbad