| 1 |
commit: 541abbcdf09e9575c2e021f5261e29b0a76a0327 |
| 2 |
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 3 |
AuthorDate: Thu Sep 1 09:52:01 2016 +0000 |
| 4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 5 |
CommitDate: Thu Sep 1 09:52:01 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=541abbcd |
| 7 |
|
| 8 |
sci-biology/brat_bw: new package, successor of sci-biology/brat |
| 9 |
|
| 10 |
Package-Manager: portage-2.3.0 |
| 11 |
|
| 12 |
sci-biology/brat_bw/brat_bw-2.0.1.ebuild | 36 ++++++++++++++++++++++++++++++++ |
| 13 |
sci-biology/brat_bw/metadata.xml | 8 +++++++ |
| 14 |
2 files changed, 44 insertions(+) |
| 15 |
|
| 16 |
diff --git a/sci-biology/brat_bw/brat_bw-2.0.1.ebuild b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild |
| 17 |
new file mode 100644 |
| 18 |
index 0000000..5060439 |
| 19 |
--- /dev/null |
| 20 |
+++ b/sci-biology/brat_bw/brat_bw-2.0.1.ebuild |
| 21 |
@@ -0,0 +1,36 @@ |
| 22 |
+# Copyright 1999-2016 Gentoo Foundation |
| 23 |
+# Distributed under the terms of the GNU General Public License v2 |
| 24 |
+# $Id$ |
| 25 |
+ |
| 26 |
+EAPI=5 |
| 27 |
+ |
| 28 |
+inherit toolchain-funcs |
| 29 |
+ |
| 30 |
+DESCRIPTION="Bisulfite-aware short read mapper, FM-index, no InDel support" |
| 31 |
+HOMEPAGE="http://compbio.cs.ucr.edu/brat/" |
| 32 |
+SRC_URI="http://compbio.cs.ucr.edu/brat/downloads/${P}.tar.gz" |
| 33 |
+ |
| 34 |
+LICENSE="GPL-3" |
| 35 |
+SLOT="0" |
| 36 |
+IUSE="" |
| 37 |
+KEYWORDS="~amd64 ~x86" |
| 38 |
+ |
| 39 |
+DEPEND="" |
| 40 |
+RDEPEND="!sci-biology/brat" |
| 41 |
+ |
| 42 |
+src_prepare() { |
| 43 |
+ sed \ |
| 44 |
+ -e "s:-Wl,-O1 : :g" \ |
| 45 |
+ -e "s:g++:$(tc-getCXX):g" \ |
| 46 |
+ -e "s:-O3:${CFLAGS} ${LDFLAGS}:g" \ |
| 47 |
+ -e "s:-w:-Wall:g" \ |
| 48 |
+ -i Makefile || die |
| 49 |
+} |
| 50 |
+ |
| 51 |
+src_install() { |
| 52 |
+ dobin brat_bw build_bw trim acgt-count remove-dupl convert_to_sam |
| 53 |
+ # possible FILLE_COLLISION with sci-biology/brat (probably some binaries just do the same) |
| 54 |
+ # dobin ${PN} ${PN}-large trim acgt-count ${PN}-large-build rev-compl check-strands remove-dupl convert-to-sam |
| 55 |
+ dodoc README |
| 56 |
+ newdoc {'User Manual BRAT_2_0_1.pdf','User_Manual_BRAT_2_0_1.pdf'} |
| 57 |
+} |
| 58 |
|
| 59 |
diff --git a/sci-biology/brat_bw/metadata.xml b/sci-biology/brat_bw/metadata.xml |
| 60 |
new file mode 100644 |
| 61 |
index 0000000..004c995 |
| 62 |
--- /dev/null |
| 63 |
+++ b/sci-biology/brat_bw/metadata.xml |
| 64 |
@@ -0,0 +1,8 @@ |
| 65 |
+<?xml version="1.0" encoding="UTF-8"?> |
| 66 |
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 67 |
+<pkgmetadata> |
| 68 |
+ <maintainer type="project"> |
| 69 |
+ <email>sci-biology@g.o</email> |
| 70 |
+ <name>Gentoo Biology Project</name> |
| 71 |
+ </maintainer> |
| 72 |
+ </pkgmetadata> |
Archives