sci-biology/blat: version bump, fix SRC_URI, update patch

Package-Manager: portage-2.2.28

4 files changed, 82 insertions, 0 deletions

diff --git a/sci-biology/blat/Manifest b/sci-biology/blat/Manifest
new file mode 100644
index 000000000..5a6ed9d73
--- /dev/null
+++ b/sci-biology/blat/Manifest
@@ -0,0 +1 @@
+DIST blatSrc36.zip 3227463 SHA256 4b0fff006c86dceb7428922bfb4f8625d78fd362d205df68e4ebba04742d2c71 SHA512 18ebd1082aa3c44739ddbf31cba05aaf2d5e83bec0884ebd40dfb775fcf06b3b404192d8a63af062373a2f7fc0ce8844cbec6b7451d8576e21ddaa76750bbd7b WHIRLPOOL 87ee398237049dbbe52ed2712a35493432a6dc559287583d5124aad66c3fbf5d356e9b91f7843f77d33450193e3c1d837bb75d4d90ca1502e36d18d31fc28aaa
diff --git a/sci-biology/blat/blat-36.ebuild b/sci-biology/blat/blat-36.ebuild
new file mode 100644
index 000000000..b420bc0c6
--- /dev/null
+++ b/sci-biology/blat/blat-36.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+MY_PN="${PN}Src"
+
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner"
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/"
+SRC_URI="http://hgwdev.cse.ucsc.edu/~kent/src/${MY_PN}${PV}.zip"
+
+SLOT="0"
+LICENSE="blat"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+S="${WORKDIR}/${MY_PN}"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+	eapply_user
+	epatch "${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/files/36-gentoo.patch b/sci-biology/blat/files/36-gentoo.patch
new file mode 100644
index 000000000..d05fe64c2
--- /dev/null
+++ b/sci-biology/blat/files/36-gentoo.patch
@@ -0,0 +1,27 @@
+--- blatSrc/inc/userApp.mk.old	2014-11-06 04:19:54.000000000 +0100
++++ blatSrc/inc/userApp.mk	2016-07-28 12:45:32.092378879 +0200
+@@ -28,11 +28,11 @@
+ objects = ${O} ${extraObjects} ${externObjects}
+ 
+ ${DESTDIR}${BINDIR}/${A}${EXE}: ${DEPLIBS} ${O} ${extraObjects}
+-	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
++	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ compile:: ${DEPLIBS} ${O} ${extraObjects}
+-	${CC} ${COPT} ${CFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
++	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm
+ 
+ install:: compile
+ 	rm -f ${DESTDIR}${BINDIR}/${A}${EXE}
+--- blatSrc/blat/makefile.old	2011-03-29 03:43:44.000000000 +0200
++++ blatSrc/blat/makefile	2016-07-28 12:41:11.905261175 +0200
+@@ -7,7 +7,7 @@
+ O = blat.o
+ 
+ blat: $O $(MYLIBS)
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
++	${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
+ 	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
+ 
+ all:
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml
new file mode 100644
index 000000000..959160fe4
--- /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>