reinit the tree, so we can have metadata

4 files changed, 263 insertions, 0 deletions

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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>