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sci-biology/blat: Remove old

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Package-Manager: Portage-2.3.4, Repoman-2.3.2
Closes: https://github.com/gentoo/gentoo/pull/4165
This commit is contained in:
David Seifert
2017-03-08 22:35:39 +01:00
parent eacdfe16dd
commit dc849f2aa3
3 changed files with 0 additions and 303 deletions
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44
sci-biology/blat/blat-34-r1.ebuild
View File

@@ -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}/"*
}

33
sci-biology/blat/blat-34.ebuild
View File

@@ -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}/"*
}

226
sci-biology/blat/files/34-gentoo.patch
View File

@@ -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: