1 |
commit: 53304a0b2f9c9ff476239218ba002c7d6c6e8b9b |
2 |
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
3 |
AuthorDate: Thu Jul 28 11:05:09 2016 +0000 |
4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
5 |
CommitDate: Thu Jul 28 11:05:09 2016 +0000 |
6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=53304a0b |
7 |
|
8 |
sci-biology/blat: version bump, fix SRC_URI, update patch |
9 |
|
10 |
Package-Manager: portage-2.2.28 |
11 |
|
12 |
sci-biology/blat/blat-36.ebuild | 46 ++++++++++++++++++++++++++++++++++ |
13 |
sci-biology/blat/files/36-gentoo.patch | 27 ++++++++++++++++++++ |
14 |
sci-biology/blat/metadata.xml | 8 ++++++ |
15 |
3 files changed, 81 insertions(+) |
16 |
|
17 |
diff --git a/sci-biology/blat/blat-36.ebuild b/sci-biology/blat/blat-36.ebuild |
18 |
new file mode 100644 |
19 |
index 0000000..b420bc0 |
20 |
--- /dev/null |
21 |
+++ b/sci-biology/blat/blat-36.ebuild |
22 |
@@ -0,0 +1,46 @@ |
23 |
+# Copyright 1999-2016 Gentoo Foundation |
24 |
+# Distributed under the terms of the GNU General Public License v2 |
25 |
+# $Id$ |
26 |
+ |
27 |
+EAPI=6 |
28 |
+ |
29 |
+inherit eutils toolchain-funcs |
30 |
+ |
31 |
+MY_PN="${PN}Src" |
32 |
+ |
33 |
+DESCRIPTION="The BLAST-Like Alignment Tool, a fast genomic sequence aligner" |
34 |
+HOMEPAGE="http://www.cse.ucsc.edu/~kent/" |
35 |
+SRC_URI="http://hgwdev.cse.ucsc.edu/~kent/src/${MY_PN}${PV}.zip" |
36 |
+ |
37 |
+SLOT="0" |
38 |
+LICENSE="blat" |
39 |
+KEYWORDS="~amd64 ~x86" |
40 |
+IUSE="" |
41 |
+ |
42 |
+S="${WORKDIR}/${MY_PN}" |
43 |
+ |
44 |
+DEPEND="app-arch/unzip" |
45 |
+RDEPEND="" |
46 |
+ |
47 |
+src_prepare() { |
48 |
+ eapply_user |
49 |
+ epatch "${FILESDIR}"/${PV}-gentoo.patch |
50 |
+ sed \ |
51 |
+ -e "1i\CFLAGS=${CFLAGS}" \ |
52 |
+ -e "1i\LDFLAGS=${LDFLAGS}" \ |
53 |
+ -i inc/common.mk || die |
54 |
+ tc-export CC |
55 |
+} |
56 |
+ |
57 |
+src_compile() { |
58 |
+ MACHTYPE=$(tc-arch) |
59 |
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
60 |
+ mkdir -p "${S}/bin/${MACHTYPE}" |
61 |
+ emake MACHTYPE="${MACHTYPE}" HOME="${S}" LDFLAGS="${LDFLAGS}" |
62 |
+} |
63 |
+ |
64 |
+src_install() { |
65 |
+ MACHTYPE=$(tc-arch) |
66 |
+ [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386" |
67 |
+ dobin "${S}/bin/${MACHTYPE}/"* |
68 |
+} |
69 |
|
70 |
diff --git a/sci-biology/blat/files/36-gentoo.patch b/sci-biology/blat/files/36-gentoo.patch |
71 |
new file mode 100644 |
72 |
index 0000000..d05fe64 |
73 |
--- /dev/null |
74 |
+++ b/sci-biology/blat/files/36-gentoo.patch |
75 |
@@ -0,0 +1,27 @@ |
76 |
+--- blatSrc/inc/userApp.mk.old 2014-11-06 04:19:54.000000000 +0100 |
77 |
++++ blatSrc/inc/userApp.mk 2016-07-28 12:45:32.092378879 +0200 |
78 |
+@@ -28,11 +28,11 @@ |
79 |
+ objects = ${O} ${extraObjects} ${externObjects} |
80 |
+ |
81 |
+ ${DESTDIR}${BINDIR}/${A}${EXE}: ${DEPLIBS} ${O} ${extraObjects} |
82 |
+- ${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm |
83 |
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm |
84 |
+ ${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE} |
85 |
+ |
86 |
+ compile:: ${DEPLIBS} ${O} ${extraObjects} |
87 |
+- ${CC} ${COPT} ${CFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm |
88 |
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${A}${EXE} ${objects} ${LINKLIBS} ${L} -lm |
89 |
+ |
90 |
+ install:: compile |
91 |
+ rm -f ${DESTDIR}${BINDIR}/${A}${EXE} |
92 |
+--- blatSrc/blat/makefile.old 2011-03-29 03:43:44.000000000 +0200 |
93 |
++++ blatSrc/blat/makefile 2016-07-28 12:41:11.905261175 +0200 |
94 |
+@@ -7,7 +7,7 @@ |
95 |
+ O = blat.o |
96 |
+ |
97 |
+ blat: $O $(MYLIBS) |
98 |
+- ${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L |
99 |
++ ${CC} ${COPT} ${CFLAGS} ${LDFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L |
100 |
+ ${STRIP} ${DESTDIR}${BINDIR}/blat${EXE} |
101 |
+ |
102 |
+ all: |
103 |
|
104 |
diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml |
105 |
new file mode 100644 |
106 |
index 0000000..959160f |
107 |
--- /dev/null |
108 |
+++ b/sci-biology/blat/metadata.xml |
109 |
@@ -0,0 +1,8 @@ |
110 |
+<?xml version="1.0" encoding="UTF-8"?> |
111 |
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
112 |
+<pkgmetadata> |
113 |
+ <maintainer type="project"> |
114 |
+ <email>sci-biology@g.o</email> |
115 |
+ <name>Gentoo Biology Project</name> |
116 |
+ </maintainer> |
117 |
+</pkgmetadata> |