Gentoo Archives: gentoo-commits

From: Horea Christian <horea.christ@×××××.com>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biobambam/
Date: Mon, 28 Sep 2020 06:06:55
Message-Id: 1601272722.7b77093ccf69b45396b77e47661ef62d9cabfdb9.chymera@gentoo
1 commit: 7b77093ccf69b45396b77e47661ef62d9cabfdb9
2 Author: Horea Christian <chr <AT> chymera <DOT> eu>
3 AuthorDate: Mon Sep 28 05:58:42 2020 +0000
4 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
5 CommitDate: Mon Sep 28 05:58:42 2020 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7b77093c
7
8 sci-biology/biobambam: removed discontinued package
9
10 Package-Manager: Portage-3.0.8, Repoman-3.0.1
11 Signed-off-by: Horea Christian <chr <AT> chymera.eu>
12
13 sci-biology/biobambam/biobambam-0.0.183.ebuild | 20 --------------------
14 sci-biology/biobambam/metadata.xml | 21 ---------------------
15 2 files changed, 41 deletions(-)
16
17 diff --git a/sci-biology/biobambam/biobambam-0.0.183.ebuild b/sci-biology/biobambam/biobambam-0.0.183.ebuild
18 deleted file mode 100644
19 index 17a247d60..000000000
20 --- a/sci-biology/biobambam/biobambam-0.0.183.ebuild
21 +++ /dev/null
22 @@ -1,20 +0,0 @@
23 -# Copyright 1999-2014 Gentoo Foundation
24 -# Distributed under the terms of the GNU General Public License v2
25 -
26 -EAPI=5
27 -
28 -FULLVER=${PV}-release-20141208165400
29 -
30 -DESCRIPTION="Tools for bam file processing"
31 -HOMEPAGE="https://github.com/gt1/biobambam"
32 -SRC_URI="https://github.com/gt1/biobambam/archive/${FULLVER}.tar.gz"
33 -
34 -LICENSE="GPL-3"
35 -SLOT="0"
36 -KEYWORDS="~x86"
37 -IUSE=""
38 -
39 -DEPEND="sci-libs/libmaus"
40 -RDEPEND="${DEPEND}"
41 -
42 -S="${WORKDIR}"/${PN}-${FULLVER}
43
44 diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml
45 deleted file mode 100644
46 index 782a697ab..000000000
47 --- a/sci-biology/biobambam/metadata.xml
48 +++ /dev/null
49 @@ -1,21 +0,0 @@
50 -<?xml version="1.0" encoding="UTF-8"?>
51 -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
52 -<pkgmetadata>
53 - <maintainer type="project">
54 - <email>sci-biology@g.o</email>
55 - <name>Gentoo Biology Project</name>
56 - </maintainer>
57 - <longdescription lang="en">
58 -This package contains some tools for processing BAM files including
59 -
60 -bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
61 -bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
62 -bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
63 -bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
64 -bamsort: reads BAM and writes BAM resorted by coordinates or query name
65 -bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
66 -</longdescription>
67 - <upstream>
68 - <remote-id type="github">gt1/biobambam</remote-id>
69 - </upstream>
70 -</pkgmetadata>