[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: cdb163b7c0a842d89160c6d6f9d298977f6a3465 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Mar 6 13:26:47 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Sat Mar 6 13:26:47 2021 + 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 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${PV}/pilon- LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64" -IUSE="" # contains bundled sbt-assembly module DEPEND=">=virtual/jdk-1.7:*"
[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: 9ec25164dc80271a01a3adeda225d91e1a96470d Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Fri Dec 14 00:24:26 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Fri Dec 14 00:24:26 2018 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ec25164 sci-biology/pilon-bin: version bump Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/pilon-bin/{pilon-bin-1.22.ebuild => pilon-bin-1.23.ebuild} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.23.ebuild similarity index 89% rename from sci-biology/pilon-bin/pilon-bin-1.22.ebuild rename to sci-biology/pilon-bin/pilon-bin-1.23.ebuild index 180d29ea5..de401bd21 100644 --- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild +++ b/sci-biology/pilon-bin/pilon-bin-1.23.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2018 Gentoo Foundation +# Copyright 1999-2018 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -16,6 +16,7 @@ SLOT="0" KEYWORDS="~amd64" IUSE="" +# contains bundled sbt-assembly module DEPEND=">=virtual/jdk-1.7:*" RDEPEND="${DEPEND} >=virtual/jre-1.7:*
[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: be15a9e01fcb68ba2f55f7392aec0d49deca8e9b Author: Justin Lecher gentoo org> AuthorDate: Mon Apr 2 12:33:57 2018 + Commit: Justin Lecher gentoo org> CommitDate: Mon Apr 2 12:33:57 2018 + 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 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;
[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: 532f43c453327e607778d2cefaf43d45e3d04de5 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Jan 21 21:46:18 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Jan 21 21:46:18 2018 + 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="${DEPEND} >=virtual/jre-1.7:* >=dev-java/htsjdk-1.130"
[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: 4f5a54734cb153fda873729addfb793bb1e0e6f6 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sun Jan 21 20:47:11 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Jan 21 20:47:11 2018 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f5a5473 sci-biology/pilon-bin: Fix java runtime version Package-Manager: Portage-2.3.19, Repoman-2.3.6 sci-biology/pilon-bin/pilon-bin-1.22.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild index 2284e6418..60019723b 100644 --- a/sci-biology/pilon-bin/pilon-bin-1.22.ebuild +++ b/sci-biology/pilon-bin/pilon-bin-1.22.ebuild @@ -17,9 +17,9 @@ KEYWORDS="~amd64" IUSE="" DEPEND="dev-java/sbt - >=virtual/jdk-1.5:*" + >=virtual/jdk-1.7:*" RDEPEND="${DEPEND} - >=virtual/jre-1.5:* + >=virtual/jre-1.7:* >=dev-java/htsjdk-1.130" S="${WORKDIR}"
[gentoo-commits] proj/sci:master commit in: sci-biology/pilon-bin/
commit: e4f568402bfead6e32904c59ce41578b7617b851 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Jan 20 21:35:57 2018 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Jan 20 21:35:57 2018 + 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 0..138cb7705 --- /dev/null +++ b/sci-biology/pilon-bin/metadata.xml @@ -0,0 +1,12 @@ + +http://www.gentoo.org/dtd/metadata.dtd;> + + + mmokr...@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biol...@gentoo.org + Gentoo Biology Project + + 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 0..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 +}