From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/blat/Manifest | 6 + sci-biology/blat/blat-34-r2.ebuild | 42 +++++ .../blat/files/blat-34-fix-build-system.patch | 207 +++++++++++++++++++++ sci-biology/blat/metadata.xml | 8 + 4 files changed, 263 insertions(+) create mode 100644 sci-biology/blat/Manifest create mode 100644 sci-biology/blat/blat-34-r2.ebuild create mode 100644 sci-biology/blat/files/blat-34-fix-build-system.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..f8a3a9fbea98 --- /dev/null +++ b/sci-biology/blat/Manifest @@ -0,0 +1,6 @@ +AUX blat-34-fix-build-system.patch 5249 SHA256 03d563305183f9b40dbc6073f7ccfaaafc0240afcd7ed70da8638c43b7e5a2eb SHA512 1c4b592ef1b45ea19d84a798f4d526c43851bf8545d4a9aaaa8842c76eff1e0e31a179d1cd914e44f67c1d5ac709b97a73a5b7e66fa680f6531efe50b6dc6246 WHIRLPOOL b878a41fba2dda93fd0dbb32e5cea634aa7bd879d9b9094b130281b98c7a953a057df512d58eda36437a78248831b7e5bde8b07fd8807144fe158efcab0b8108 +DIST blatSrc34.zip 2142975 SHA256 b764828fdf8ef4c9994ae4b6148340a776493475edb573b6adf63ae7ca9b2629 SHA512 67a1dc9a93d8ddee0fca7ce94096ecfffc71d4e0697afb285f4b64205e9eb62150a145375c29dd1ccb3cea8e8a7a71a817c8e73d7aba3e97616f1606b751afe8 WHIRLPOOL eace9c1befa8b3b019f0adc6047429fcede604c380ae52522efadb69dea2de4fb7878e961895abe7eebfcdc9a4c40ba16bb9479f13b16fde7f720933ebb7f323 +EBUILD blat-34-r2.ebuild 807 SHA256 e839e891e5bd99dc37fc667ec154c7a168eb31341860d15112dbff2fef24594b SHA512 451b189b505331cd7c045fc19982d55d11673afdfa8f0f9bd2b57cd23097c5a066afe477d973a0f30e1a47a8d1893abc552ef8ccc5f59ce9f3a66e0ceedc94b2 WHIRLPOOL 0b72a2d14033b09e692f8ce1d9391dc0e8f6433057b54810f1827625e811e122374a95fe7f88e1e23ecc1dda83329ba034e5395f6c99ffe4101949facc17f970 +MISC ChangeLog 2485 SHA256 a8b3f5d2e60062ccbc233f2b11ea21b4bbf3869c1cbe9e16c656438493f1cdca SHA512 4c4025e50e831076ab02eb8ea2e11fd1e0800ea6c5d50df6065c914dd72c9c3e09f10b55f520f2c24cef8a50383f694cbed6a53521209892460e3d074415b274 WHIRLPOOL 5e15c6c391137f039ea202277f9361b05b8dc447fa7709d7f7c10a9054b1c0ea2f30ab400fee42dbb1ff26e19324a2f2a6349b0a7a8b8db2f1940ea2cf32cb89 +MISC ChangeLog-2015 831 SHA256 727ef35729a38580c3b0ee1094570a011bd5ef617a4a532d780523f8bc03f7de SHA512 702193bebc1a967f6a4c9f6f72e380cfeec2ffc19885a367c1356b7fbf4eac4ed8acb20da023a5c2e38f6e5cf5ffa0e72a362c80b98c3ead24d1a44625a49c97 WHIRLPOOL 831cb7a9b8e69891f0922250c7ee68b65c9f4416e6e5c38c93a819f34b45371606dccc2cf0ea96c29cfda3d08f7951d4d45b5fe97f87f890f73e3c1fb5539fc6 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/blat/blat-34-r2.ebuild b/sci-biology/blat/blat-34-r2.ebuild new file mode 100644 index 000000000000..e10bc367a311 --- /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 000000000000..361149cc1211 --- /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: diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/blat/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-biology@gentoo.org + Gentoo Biology Project + + -- cgit v1.2.3