* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2018-01-20 21:36 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-01-20 21:36 UTC (permalink / raw
To: gentoo-commits
commit: e4f568402bfead6e32904c59ce41578b7617b851
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:35:57 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:35:57 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e4f56840
sci-biology/pilon-bin: new, albeit binary package
The sources are in scala language, btw.
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/pilon-bin/metadata.xml | 12 ++++++++++++
sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 30 +++++++++++++++++++++++++++++
2 files changed, 42 insertions(+)
diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/pilon-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>
diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
new file mode 100644
index 000000000..2284e6418
--- /dev/null
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-2
+
+DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
+HOMEPAGE="https://github.com/broadinstitute/pilon
+ https://github.com/broadinstitute/pilon/wiki"
+SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-java/sbt
+ >=virtual/jdk-1.5:*"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.5:*
+ >=dev-java/htsjdk-1.130"
+
+S="${WORKDIR}"
+
+src_install(){
+ cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
+ java-pkg_dojar pilon-${PV}.jar
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2018-01-21 20:47 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-01-21 20:47 UTC (permalink / raw
To: gentoo-commits
commit: 4f5a54734cb153fda873729addfb793bb1e0e6f6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 21 20:47:11 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 21 20:47:11 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f5a5473
sci-biology/pilon-bin: Fix java runtime version
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
index 2284e6418..60019723b 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -17,9 +17,9 @@ KEYWORDS="~amd64"
IUSE=""
DEPEND="dev-java/sbt
- >=virtual/jdk-1.5:*"
+ >=virtual/jdk-1.7:*"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5:*
+ >=virtual/jre-1.7:*
>=dev-java/htsjdk-1.130"
S="${WORKDIR}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2018-01-21 21:46 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-01-21 21:46 UTC (permalink / raw
To: gentoo-commits
commit: 532f43c453327e607778d2cefaf43d45e3d04de5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 21 21:46:18 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 21 21:46:18 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=532f43c4
sci-biology/pilon-bin: Drop the scala dependency for binary build
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
index 60019723b..feeafa365 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -16,8 +16,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="dev-java/sbt
- >=virtual/jdk-1.7:*"
+DEPEND=">=virtual/jdk-1.7:*"
RDEPEND="${DEPEND}
>=virtual/jre-1.7:*
>=dev-java/htsjdk-1.130"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2018-04-02 12:45 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2018-04-02 12:45 UTC (permalink / raw
To: gentoo-commits
commit: be15a9e01fcb68ba2f55f7392aec0d49deca8e9b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 2 12:33:57 2018 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 2 12:33:57 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=be15a9e0
sci-biology/pilon-bin: FIX Stale CVS header on line: 3
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
Package-Manager: Portage-2.3.27, Repoman-2.3.9
sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
index feeafa365..180d29ea5 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
@@ -1,13 +1,13 @@
# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Id$
EAPI=6
inherit java-pkg-2
DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
-HOMEPAGE="https://github.com/broadinstitute/pilon
+HOMEPAGE="
+ https://github.com/broadinstitute/pilon
https://github.com/broadinstitute/pilon/wiki"
SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2018-12-14 0:24 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-12-14 0:24 UTC (permalink / raw
To: gentoo-commits
commit: 9ec25164dc80271a01a3adeda225d91e1a96470d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 14 00:24:26 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 14 00:24:26 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ec25164
sci-biology/pilon-bin: version bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/pilon-bin/{pilon-bin-1.22.ebuild => pilon-bin-1.23.ebuild} | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.23.ebuild
similarity index 89%
rename from sci-biology/pilon-bin/pilon-bin-1.22.ebuild
rename to sci-biology/pilon-bin/pilon-bin-1.23.ebuild
index 180d29ea5..de401bd21 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.23.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -16,6 +16,7 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
+# contains bundled sbt-assembly module
DEPEND=">=virtual/jdk-1.7:*"
RDEPEND="${DEPEND}
>=virtual/jre-1.7:*
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
@ 2021-03-06 13:35 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 13:35 UTC (permalink / raw
To: gentoo-commits
commit: cdb163b7c0a842d89160c6d6f9d298977f6a3465
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 13:26:47 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 13:26:47 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cdb163b7
sci-biology/pilon-bin: version bump, EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../pilon-bin/{pilon-bin-1.23.ebuild => pilon-bin-1.24.ebuild} | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pilon-bin/pilon-bin-1.23.ebuild b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
similarity index 92%
rename from sci-biology/pilon-bin/pilon-bin-1.23.ebuild
rename to sci-biology/pilon-bin/pilon-bin-1.24.ebuild
index de401bd21..49d15366f 100644
--- a/sci-biology/pilon-bin/pilon-bin-1.23.ebuild
+++ b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit java-pkg-2
@@ -14,7 +14,6 @@ SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
# contains bundled sbt-assembly module
DEPEND=">=virtual/jdk-1.7:*"
^ permalink raw reply related [flat|nested] 6+ messages in thread
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