Get Gentoo!
gentoo.org sites
gentoo.org Wiki Bugs Forums Packages
Planet Archives Sources
Infra Status
summaryrefslogtreecommitdiff
path: root/sci-biology/blat
diff options
context:
space:
mode:
Diffstat (limited to 'sci-biology/blat')
-rw-r--r--sci-biology/blat/blat-34-r1.ebuild44
-rw-r--r--sci-biology/blat/blat-34.ebuild33
-rw-r--r--sci-biology/blat/files/34-gentoo.patch226
3 files changed, 0 insertions, 303 deletions
diff --git a/sci-biology/blat/blat-34-r1.ebuild b/sci-biology/blat/blat-34-r1.ebuild
deleted file mode 100644
index 52079d22bea9..000000000000
--- a/sci-biology/blat/blat-34-r1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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/${MACHTYPE}/"*
-}
diff --git a/sci-biology/blat/blat-34.ebuild b/sci-biology/blat/blat-34.ebuild
deleted file mode 100644
index 3ec0eb05bdb8..000000000000
--- a/sci-biology/blat/blat-34.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-inherit toolchain-funcs
-
-DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
-LICENSE="blat"
-HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-MY_PN="${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
deleted file mode 100644
index 8bdd05bff68d..000000000000
--- a/sci-biology/blat/files/34-gentoo.patch
+++ /dev/null
@@ -1,226 +0,0 @@
- 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: