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

2014-12-26 Thread Justin Lecher 
commit: e0612e71901f1c95173fba536cba4fe33bdffbff
Author: mschubert mschu.dev AT gmail DOT com
AuthorDate: Sat Dec 20 19:29:09 2014 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sat Dec 20 19:29:09 2014 +
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/

2014-12-26 Thread Justin Lecher 
commit: be2f4981d032c159c47549e819b668772b468566
Author: mschubert mschu.dev AT gmail DOT com
AuthorDate: Sat Dec 20 20:00:02 2014 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sat Dec 20 20:00:02 2014 +
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 000..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
+herdsci-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 000..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
+herdsci-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/

2014-12-26 Thread Justin Lecher 
commit: 721baf79f8fa56e89a9e05a129eae5adc4a39f49
Author: mschubert mschu.dev AT gmail DOT com
AuthorDate: Sun Dec 21 15:10:02 2014 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sun Dec 21 15:10:02 2014 +
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}