* [gentoo-commits] proj/sci:master commit in: sci-biology/Jannovar-bin/
@ 2015-05-05 14:29 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-05-05 14:29 UTC (permalink / raw
To: gentoo-commits
commit: df363e30c8033d85992c787537f5864836ebf4b4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 5 14:29:02 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 5 14:29:02 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=df363e30
sci-biology/Jannovar-bin: new package
Package-Manager: portage-2.2.18
sci-biology/Jannovar-bin/ChangeLog | 9 +++++++
.../Jannovar-bin/Jannovar-bin-20150503.ebuild | 30 ++++++++++++++++++++++
sci-biology/Jannovar-bin/metadata.xml | 9 +++++++
3 files changed, 48 insertions(+)
diff --git a/sci-biology/Jannovar-bin/ChangeLog b/sci-biology/Jannovar-bin/ChangeLog
new file mode 100644
index 0000000..5a6ec92
--- /dev/null
+++ b/sci-biology/Jannovar-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/Jannovar-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Jannovar-bin-20150503 (05 May 2015)
+
+ 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +Jannovar-bin-20150503.ebuild, +metadata.xml:
+ sci-biology/Jannovar-bin: new package
diff --git a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
new file mode 100644
index 0000000..890494a
--- /dev/null
+++ b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool"
+HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"
+SRC_URI="http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/Jannovar.jar -> Jannovar-bin-20150503.jar
+ http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/JannovarTutorial.pdf -> JannovarTutorial.pdf
+ http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/tutorial.tgz -> Jannovar_tutorial.tgz"
+
+# https://github.com/charite/jannovar
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}"
+
+src_install(){
+ cp "${DISTDIR}"/Jannovar-bin-20150503.jar Jannovar-bin.jar
+ java-pkg_newjar Jannovar-bin.jar
+ java-pkg_dolauncher Jannovar-bin --jar Jannovar-bin.jar
+}
diff --git a/sci-biology/Jannovar-bin/metadata.xml b/sci-biology/Jannovar-bin/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Jannovar-bin/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] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/
@ 2016-06-23 15:16 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-06-23 15:16 UTC (permalink / raw
To: gentoo-commits
commit: 5b8e34465714552fcfb87a2bce4b6ecb2ac216b8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 15:15:48 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 15:15:48 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b8e3446
sci-biology/jannovar-bin: renamed package; version bump
Package-Manager: portage-2.2.28
sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 28 +++++++++++++++++++++++
sci-biology/jannovar-bin/metadata.xml | 12 ++++++++++
2 files changed, 40 insertions(+)
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
new file mode 100644
index 0000000..fc706b8
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool"
+HOMEPAGE="http://compbio.charite.de
+ https://github.com/charite/jannovar"
+SRC_URI="https://github.com/charite/jannovar/releases/download/v0.16/jannovar-cli-0.16.jar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
+
+S="${WORKDIR}"
+
+src_install(){
+ cp "${DISTDIR}"/jannovar-cli-0.16.jar jannovar-bin.jar
+ java-pkg_newjar jannovar-bin.jar
+ java-pkg_dolauncher jannovar-bin --jar jannovar-bin.jar
+}
diff --git a/sci-biology/jannovar-bin/metadata.xml b/sci-biology/jannovar-bin/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/jannovar-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+<maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/
@ 2016-06-23 16:26 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-06-23 16:26 UTC (permalink / raw
To: gentoo-commits
commit: 1ee22ba11c2bd964ef4270f4f31733b4b22254a2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 16:26:08 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 16:26:08 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ee22ba1
sci-biology/jannovar-bin: drop KEYWORDS as the launchers point to non-existing jar files
Package-Manager: portage-2.2.28
sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
index fc706b8..aee7faa 100644
--- a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -9,20 +9,25 @@ inherit java-pkg-2
DESCRIPTION="Exome annotation tool"
HOMEPAGE="http://compbio.charite.de
https://github.com/charite/jannovar"
-SRC_URI="https://github.com/charite/jannovar/releases/download/v0.16/jannovar-cli-0.16.jar"
+SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-cli-${PV}.jar
+ https://repo1.maven.org/maven2/de/charite/compbio/jped-cli/${PV}/jped-cli-${PV}.jar"
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
+DEPEND=">=virtual/jdk-1.6"
+RDEPEND=">=virtual/jre-1.6"
S="${WORKDIR}"
+# BUG: the two jar file soverwrite each other somehow during install
src_install(){
- cp "${DISTDIR}"/jannovar-cli-0.16.jar jannovar-bin.jar
- java-pkg_newjar jannovar-bin.jar
- java-pkg_dolauncher jannovar-bin --jar jannovar-bin.jar
+ cp "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli-bin.jar
+ java-pkg_newjar jannovar-cli-bin.jar
+ java-pkg_dolauncher jannovar-bin --jar jannovar-cli-"${PV}".jar
+ cp "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli-bin.jar
+ java-pkg_newjar jped-cli-bin.jar
+ java-pkg_dolauncher jped-cli-bin --jar jped-cli-"${PV}".jar
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/
@ 2016-06-23 16:37 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-06-23 16:37 UTC (permalink / raw
To: gentoo-commits
commit: a30c6ba70f9f17451b5a5d0d481c0f0f28d17e7b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 16:37:07 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 16:37:07 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a30c6ba7
sci-biology/jannovar-bin: add KEYWORDS, works now
Package-Manager: portage-2.2.28
sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
index aee7faa..4d56e65 100644
--- a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -14,7 +14,7 @@ SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-c
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND=">=virtual/jdk-1.6"
@@ -22,12 +22,9 @@ RDEPEND=">=virtual/jre-1.6"
S="${WORKDIR}"
-# BUG: the two jar file soverwrite each other somehow during install
src_install(){
- cp "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli-bin.jar
- java-pkg_newjar jannovar-cli-bin.jar
- java-pkg_dolauncher jannovar-bin --jar jannovar-cli-"${PV}".jar
- cp "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli-bin.jar
- java-pkg_newjar jped-cli-bin.jar
- java-pkg_dolauncher jped-cli-bin --jar jped-cli-"${PV}".jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
+ java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
+ java-pkg_newjar "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli.jar
+ java-pkg_dolauncher jped-cli-bin --jar jped-cli.jar
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Jannovar-bin/
@ 2016-11-15 20:20 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-11-15 20:20 UTC (permalink / raw
To: gentoo-commits
commit: b2815a91492bff320b83e10cd510b04b2186de27
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 15 20:20:03 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 15 20:20:03 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b2815a91
sci-biology/Jannovar-bin: replaced by sci-biology/jannovar, deleting
.../Jannovar-bin/Jannovar-bin-20150503.ebuild | 30 ----------------------
sci-biology/Jannovar-bin/metadata.xml | 12 ---------
2 files changed, 42 deletions(-)
diff --git a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
deleted file mode 100644
index 09efa5d..0000000
--- a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Exome annotation tool"
-HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"
-SRC_URI="http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/Jannovar.jar -> Jannovar-bin-20150503.jar
- http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/JannovarTutorial.pdf -> JannovarTutorial.pdf
- http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/tutorial.tgz -> Jannovar_tutorial.tgz"
-
-# https://github.com/charite/jannovar
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.7"
-RDEPEND=">=virtual/jre-1.7"
-
-S="${WORKDIR}"
-
-src_install(){
- cp "${DISTDIR}"/Jannovar-bin-20150503.jar Jannovar-bin.jar
- java-pkg_newjar Jannovar-bin.jar
- java-pkg_dolauncher Jannovar-bin --jar Jannovar-bin.jar
-}
diff --git a/sci-biology/Jannovar-bin/metadata.xml b/sci-biology/Jannovar-bin/metadata.xml
deleted file mode 100644
index 1699e58..0000000
--- a/sci-biology/Jannovar-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
-<maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/
@ 2016-12-04 20:15 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-12-04 20:15 UTC (permalink / raw
To: gentoo-commits
commit: 18cc3c3dfef3fb76ed1be70c6726b57e5f40f337
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec 4 20:15:06 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec 4 20:15:06 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=18cc3c3d
sci-biology/jannovar-bin: version bump
Provided sci-biology/jannovar download through maven lots of dependencies
and anyway uses plenty of upstream jar file this sci-biology/jannovar-bin
package is probably better choice due to size of downloads and security
Package-Manager: portage-2.3.2
sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild | 30 ------------------
sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild | 37 +++++++++++++++++++++++
2 files changed, 37 insertions(+), 30 deletions(-)
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
deleted file mode 100644
index 4d56e65..0000000
--- a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit java-pkg-2
-
-DESCRIPTION="Exome annotation tool"
-HOMEPAGE="http://compbio.charite.de
- https://github.com/charite/jannovar"
-SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-cli-${PV}.jar
- https://repo1.maven.org/maven2/de/charite/compbio/jped-cli/${PV}/jped-cli-${PV}.jar"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=">=virtual/jdk-1.6"
-RDEPEND=">=virtual/jre-1.6"
-
-S="${WORKDIR}"
-
-src_install(){
- java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
- java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
- java-pkg_newjar "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli.jar
- java-pkg_dolauncher jped-cli-bin --jar jped-cli.jar
-}
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
new file mode 100644
index 0000000..e6f392e
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool (upstream jar binaries)"
+HOMEPAGE="http://compbio.charite.de
+ https://github.com/charite/jannovar"
+SRC_URI="https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-vardbs/${PV}/jannovar-vardbs-${PV}.jar
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-htsjdk/${PV}/jannovar-htsjdk-${PV}.jar
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-inheritance-checker/${PV}/jannovar-inheritance-checker-${PV}.jar
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-core/${PV}/jannovar-core-${PV}.jar
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-hgvs/${PV}/jannovar-hgvs-${PV}.jar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6"
+RDEPEND=">=virtual/jre-1.6"
+
+S="${WORKDIR}"
+
+src_install(){
+ java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
+ java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-vardbs-"${PV}".jar jannovar-vardbs.jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-htsjdk-"${PV}".jar jannovar-htsjdk.jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-inheritance-checker-"${PV}".jar jannovar-inheritance-checker.jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-core-${PV}.jar jannovar-core.jar
+ java-pkg_newjar "${DISTDIR}"/jannovar-hgvs-${PV}.jar jannovar-hgvs.jar
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/
@ 2021-01-19 13:04 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 13:04 UTC (permalink / raw
To: gentoo-commits
commit: 89e43de4283587a68e29f49392474fbc59c23b73
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 13:04:18 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 13:04:18 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89e43de4
sci-biology/jannovar-bin: version bump 0.35, unmask
remove non-bin version, maven is not supported by portage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
...annovar-bin-0.17.ebuild => jannovar-bin-0.35.ebuild} | 17 +++++++----------
1 file changed, 7 insertions(+), 10 deletions(-)
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
similarity index 71%
rename from sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
rename to sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
index 4544eaab8..1b3a90297 100644
--- a/sci-biology/jannovar-bin/jannovar-bin-0.17.ebuild
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.35.ebuild
@@ -1,27 +1,25 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit java-pkg-2
DESCRIPTION="Exome annotation tool (upstream jar binaries)"
-HOMEPAGE="http://compbio.charite.de
- https://github.com/charite/jannovar"
-SRC_URI="https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
+HOMEPAGE="https://jannovar.readthedocs.io/en/master/"
+SRC_URI="
+ https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-cli/${PV}/jannovar-cli-${PV}.jar
https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-vardbs/${PV}/jannovar-vardbs-${PV}.jar
https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-htsjdk/${PV}/jannovar-htsjdk-${PV}.jar
- https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-inheritance-checker/${PV}/jannovar-inheritance-checker-${PV}.jar
https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-core/${PV}/jannovar-core-${PV}.jar
https://search.maven.org/remotecontent?filepath=de/charite/compbio/jannovar-hgvs/${PV}/jannovar-hgvs-${PV}.jar"
LICENSE="BSD-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-DEPEND=">=virtual/jdk-1.6"
-RDEPEND=">=virtual/jre-1.6"
+DEPEND=">=virtual/jdk-1.7"
+RDEPEND=">=virtual/jre-1.7"
S="${WORKDIR}"
@@ -30,7 +28,6 @@ src_install(){
java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
java-pkg_newjar "${DISTDIR}"/jannovar-vardbs-"${PV}".jar jannovar-vardbs.jar
java-pkg_newjar "${DISTDIR}"/jannovar-htsjdk-"${PV}".jar jannovar-htsjdk.jar
- java-pkg_newjar "${DISTDIR}"/jannovar-inheritance-checker-"${PV}".jar jannovar-inheritance-checker.jar
java-pkg_newjar "${DISTDIR}"/jannovar-core-${PV}.jar jannovar-core.jar
java-pkg_newjar "${DISTDIR}"/jannovar-hgvs-${PV}.jar jannovar-hgvs.jar
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2021-01-19 13:04 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-06-23 15:16 [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2021-01-19 13:04 Andrew Ammerlaan
2016-12-04 20:15 Martin Mokrejs
2016-11-15 20:20 [gentoo-commits] proj/sci:master commit in: sci-biology/Jannovar-bin/ Martin Mokrejs
2016-06-23 16:37 [gentoo-commits] proj/sci:master commit in: sci-biology/jannovar-bin/ Martin Mokrejs
2016-06-23 16:26 Martin Mokrejs
2015-05-05 14:29 [gentoo-commits] proj/sci:master commit in: sci-biology/Jannovar-bin/ Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox