[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus/, sci-biology/biobambam/

[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus/, sci-biology/biobambam/

[Justin Lecher]

commit:     e0612e71901f1c95173fba536cba4fe33bdffbff
Author:     mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Dec 20 19:29:09 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 20 19:29:09 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e0612e71

fix license: GPL-3

---
 sci-biology/biobambam/biobambam-0.0.183.ebuild | 2 +-
 sci-libs/libmaus/libmaus-0.0.185.ebuild        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/biobambam/biobambam-0.0.183.ebuild b/sci-biology/biobambam/biobambam-0.0.183.ebuild
index 0c9b1be..ffe9d94 100644
--- a/sci-biology/biobambam/biobambam-0.0.183.ebuild
+++ b/sci-biology/biobambam/biobambam-0.0.183.ebuild
@@ -11,7 +11,7 @@ DESCRIPTION="Tools for bam file processing"
 HOMEPAGE="https://github.com/gt1/biobambam"
 SRC_URI="https://github.com/gt1/biobambam/archive/${FULLVER}.tar.gz"
 
-LICENSE="GPLv3"
+LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~x86"
 IUSE=""

diff --git a/sci-libs/libmaus/libmaus-0.0.185.ebuild b/sci-libs/libmaus/libmaus-0.0.185.ebuild
index fa5adde..b8fc89a 100644
--- a/sci-libs/libmaus/libmaus-0.0.185.ebuild
+++ b/sci-libs/libmaus/libmaus-0.0.185.ebuild
@@ -11,7 +11,7 @@ DESCRIPTION="Library for biobambam"
 HOMEPAGE="https://github.com/gt1/libmaus"
 SRC_URI="https://github.com/gt1/libmaus/archive/${FULLVER}.tar.gz"
 
-LICENSE="GPLv3"
+LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~x86"
 IUSE=""

[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus/, sci-biology/biobambam/

[Justin Lecher]

commit:     be2f4981d032c159c47549e819b668772b468566
Author:     mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Dec 20 20:00:02 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Dec 20 20:00:02 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=be2f4981

add metadata.xml

---
 sci-biology/biobambam/metadata.xml | 15 +++++++++++++++
 sci-libs/libmaus/metadata.xml      | 14 ++++++++++++++
 2 files changed, 29 insertions(+)

diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml
new file mode 100644
index 0000000..9dab650
--- /dev/null
+++ b/sci-biology/biobambam/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+<longdescription lang="en">
+This package contains some tools for processing BAM files including
+
+bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
+bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
+bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
+bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
+bamsort: reads BAM and writes BAM resorted by coordinates or query name
+bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
+</longdescription>
+</pkgmetadata>

diff --git a/sci-libs/libmaus/metadata.xml b/sci-libs/libmaus/metadata.xml
new file mode 100644
index 0000000..3d92636
--- /dev/null
+++ b/sci-libs/libmaus/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-libs</herd>
+<longdescription lang="en">
+libmaus is a collection of data structures and algorithms. It contains
+
+I/O classes (single byte and UTF-8)
+	bitio classes (input, output and various forms of bit level manipulation)
+	text indexing classes (suffix and LCP array, fulltext and minute (FM), ...)
+	BAM sequence alignment files input/output (simple and collating)
+	and many lower level support classes.
+</longdescription>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus/, sci-biology/biobambam/

[Justin Lecher]

commit:     721baf79f8fa56e89a9e05a129eae5adc4a39f49
Author:     mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sun Dec 21 15:10:02 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 21 15:10:02 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=721baf79

drop autotools-utils, empty DEPEND

---
 sci-biology/biobambam/biobambam-0.0.183.ebuild | 1 -
 sci-libs/libmaus/libmaus-0.0.185.ebuild        | 4 ----
 2 files changed, 5 deletions(-)

diff --git a/sci-biology/biobambam/biobambam-0.0.183.ebuild b/sci-biology/biobambam/biobambam-0.0.183.ebuild
index ffe9d94..f61de36 100644
--- a/sci-biology/biobambam/biobambam-0.0.183.ebuild
+++ b/sci-biology/biobambam/biobambam-0.0.183.ebuild
@@ -3,7 +3,6 @@
 # $Header: $
 
 EAPI=5
-inherit autotools-utils
 
 FULLVER=${PV}-release-20141208165400
 

diff --git a/sci-libs/libmaus/libmaus-0.0.185.ebuild b/sci-libs/libmaus/libmaus-0.0.185.ebuild
index b8fc89a..b221963 100644
--- a/sci-libs/libmaus/libmaus-0.0.185.ebuild
+++ b/sci-libs/libmaus/libmaus-0.0.185.ebuild
@@ -3,7 +3,6 @@
 # $Header: $
 
 EAPI=5
-inherit autotools-utils
 
 FULLVER=${PV}-release-20141201090944
 
@@ -16,7 +15,4 @@ SLOT="0"
 KEYWORDS="~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}"/${PN}-${FULLVER}