* [gentoo-commits] proj/sci:master commit in: sci-biology/bambino/
@ 2014-03-23 18:16 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2014-03-23 18:16 UTC (permalink / raw
To: gentoo-commits
commit: a7bf4e9d7d31c5c27213f618b1160b0d7006ac1c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 18:15:12 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 18:15:12 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7bf4e9d
sci-biology/bambino: a new package, maybe should have -bin in its name?; needs decent inspection from java team for sure
Package-Manager: portage-2.2.7
---
sci-biology/bambino/ChangeLog | 11 ++++++++++
sci-biology/bambino/bambino-1.02.ebuild | 36 +++++++++++++++++++++++++++++++++
sci-biology/bambino/bambino-1.06.ebuild | 36 +++++++++++++++++++++++++++++++++
sci-biology/bambino/metadata.xml | 9 +++++++++
4 files changed, 92 insertions(+)
diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog
new file mode 100644
index 0000000..1cc049f
--- /dev/null
+++ b/sci-biology/bambino/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/bambino
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bambino-1.02 (23 Mar 2014)
+*bambino-1.06 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +bambino-1.02.ebuild, +bambino-1.06.ebuild, +metadata.xml:
+ sci-biology/bambino: a new package, maybe should have -bin in its name?; needs
+ decent inspection from java team for sure
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
new file mode 100644
index 0000000..4ea6c9d
--- /dev/null
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 eutils
+
+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+
+# bug #377305
+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar
+ https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.02.jar"
+
+LICENSE="bambino"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=virtual/jdk-1.6
+ sci-biology/picard
+ dev-java/jdbc-mysql"
+
+src_install(){
+ insinto "${DESTDIR}"/usr/share/"${PN}"/lib
+ doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
+ doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+
+ einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'"
+ einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'"
+ einfo "More info at "${HOMEPAGE}
+
+}
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
new file mode 100644
index 0000000..864beee
--- /dev/null
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 eutils
+
+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+
+# bug #377305
+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar
+ https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.06.jar"
+
+LICENSE="bambino"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=virtual/jdk-1.6
+ sci-biology/picard
+ dev-java/jdbc-mysql"
+
+src_install(){
+ insinto "${DESTDIR}"/usr/share/"${PN}"/lib
+ doins "${DISTDIR}"/bambino_core_"${PV}".jar || die
+ doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die
+
+ einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'"
+ einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'"
+ einfo "More info at "${HOMEPAGE}
+
+}
diff --git a/sci-biology/bambino/metadata.xml b/sci-biology/bambino/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/bambino/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambino/
@ 2014-03-23 18:23 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2014-03-23 18:23 UTC (permalink / raw
To: gentoo-commits
commit: ab02d7eac1855f385321a62bf372ed25384d1d87
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 18:22:12 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 18:22:12 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ab02d7ea
sci-biology/bambino: added more relevant homepage with some INSTALL info
Package-Manager: portage-2.2.7
---
sci-biology/bambino/ChangeLog | 4 ++++
sci-biology/bambino/bambino-1.02.ebuild | 3 ++-
sci-biology/bambino/bambino-1.06.ebuild | 3 ++-
3 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog
index 1cc049f..5b8945a 100644
--- a/sci-biology/bambino/ChangeLog
+++ b/sci-biology/bambino/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild,
+ bambino-1.06.ebuild:
+ sci-biology/bambino: added more relevant homepage with some INSTALL info
+
*bambino-1.02 (23 Mar 2014)
*bambino-1.06 (23 Mar 2014)
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
index 4ea6c9d..a94945b 100644
--- a/sci-biology/bambino/bambino-1.02.ebuild
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -7,7 +7,8 @@ EAPI=3
inherit java-pkg-2 eutils
DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
-HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
+ https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
# bug #377305
SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
index 864beee..a6fb63a 100644
--- a/sci-biology/bambino/bambino-1.06.ebuild
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -7,7 +7,8 @@ EAPI=3
inherit java-pkg-2 eutils
DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
-HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html"
+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
+ https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
# bug #377305
SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambino/
@ 2014-09-16 17:50 Christoph Junghans
0 siblings, 0 replies; 4+ messages in thread
From: Christoph Junghans @ 2014-09-16 17:50 UTC (permalink / raw
To: gentoo-commits
commit: 2a106064fb638352231061100d67006b5ba3f8d0
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 17:26:49 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 17:26:49 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a106064
fixed DESCRIPTION
Package-Manager: portage-2.2.8-r1
---
sci-biology/bambino/ChangeLog | 4 ++++
sci-biology/bambino/bambino-1.02.ebuild | 4 ++--
sci-biology/bambino/bambino-1.06.ebuild | 4 ++--
3 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog
index 5b8945a..ddfd6be 100644
--- a/sci-biology/bambino/ChangeLog
+++ b/sci-biology/bambino/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> bambino-1.02.ebuild,
+ bambino-1.06.ebuild:
+ fixed DESCRIPTION
+
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild,
bambino-1.06.ebuild:
sci-biology/bambino: added more relevant homepage with some INSTALL info
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
index a94945b..2a6d7f5 100644
--- a/sci-biology/bambino/bambino-1.02.ebuild
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -2,11 +2,11 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
inherit java-pkg-2 eutils
-DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+DESCRIPTION="display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
index a6fb63a..c717ffe 100644
--- a/sci-biology/bambino/bambino-1.06.ebuild
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -2,11 +2,11 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
inherit java-pkg-2 eutils
-DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
+DESCRIPTION="display SAM/BAM files and for SNP/indel detection, report coverage in .wig files"
HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html
https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/bam_utils.html"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bambino/
@ 2015-03-13 12:32 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-03-13 12:32 UTC (permalink / raw
To: gentoo-commits
commit: 32dbb8a87e63d395a03109dab9ed4923bb8db0d4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 13 12:31:55 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 13 12:31:55 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=32dbb8a8
fix java dependencies syntax
Package-Manager: portage-2.2.15
sci-biology/bambino/ChangeLog | 6 +++++-
sci-biology/bambino/bambino-1.02.ebuild | 6 +++---
sci-biology/bambino/bambino-1.06.ebuild | 6 +++---
3 files changed, 11 insertions(+), 7 deletions(-)
diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog
index ddfd6be..0078ba7 100644
--- a/sci-biology/bambino/ChangeLog
+++ b/sci-biology/bambino/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/bambino
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild,
+ bambino-1.06.ebuild:
+ fix java dependencies syntax
+
16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> bambino-1.02.ebuild,
bambino-1.06.ebuild:
fixed DESCRIPTION
diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild
index 2a6d7f5..1fd268d 100644
--- a/sci-biology/bambino/bambino-1.02.ebuild
+++ b/sci-biology/bambino/bambino-1.02.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -19,9 +19,9 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=""
+DEPEND=">=virtual/jdk-1.6:*"
RDEPEND="${DEPEND}
- >=virtual/jdk-1.6
+ >=virtual/jre-1.6:*
sci-biology/picard
dev-java/jdbc-mysql"
diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild
index c717ffe..b13b855 100644
--- a/sci-biology/bambino/bambino-1.06.ebuild
+++ b/sci-biology/bambino/bambino-1.06.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -19,9 +19,9 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=""
+DEPEND=">=virtual/jdk-1.6:*"
RDEPEND="${DEPEND}
- >=virtual/jdk-1.6
+ >=virtual/jre-1.6:*
sci-biology/picard
dev-java/jdbc-mysql"
^ permalink raw reply related [flat|nested] 4+ messages in thread
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