* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2021-01-10 12:27 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 12:27 UTC (permalink / raw
To: gentoo-commits
commit: ff0b693761a9db367f9c83fa4bd2c0a08fba8cfa
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 12:23:44 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 12:23:44 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ff0b6937
sci-biology/NGSEPcore: add slot operator
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
index 7dc343127..e001d175b 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -17,7 +17,7 @@ LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-RDEPEND=">=virtual/jdk-1.8"
+RDEPEND=">=virtual/jdk-1.8:="
DEPEND="${RDEPEND}"
S="${WORKDIR}/${PN}_${PV}"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2025-01-10 14:43 Alexander Puck Neuwirth
0 siblings, 0 replies; 6+ messages in thread
From: Alexander Puck Neuwirth @ 2025-01-10 14:43 UTC (permalink / raw
To: gentoo-commits
commit: c74740d4a85e75cb9e02d081facd829fabee19ab
Author: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
AuthorDate: Fri Jan 10 10:03:36 2025 +0000
Commit: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de>
CommitDate: Fri Jan 10 14:43:02 2025 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c74740d4
sci-biology/NGSEPcore: rm non versioned documentation
Signed-off-by: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik.de>
sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 13 +++----------
sci-biology/NGSEPcore/metadata.xml | 1 +
2 files changed, 4 insertions(+), 10 deletions(-)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
index 022f39cf1..1ae0fec8a 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -8,11 +8,9 @@ inherit java-pkg-2
DESCRIPTION="NGSEP (CNV and indel discovery)"
HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
https://github.com/NGSEP/NGSEPcore"
-SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
- https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.pdf -> ${P}_UserManual.pdf
- https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
- https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+SRC_URI="https://downloads.sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz"
+S="${WORKDIR}/${PN}_${PV}"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
@@ -20,8 +18,6 @@ KEYWORDS="~amd64 ~x86"
RDEPEND=">=virtual/jdk-1.8:="
DEPEND="${RDEPEND}"
-S="${WORKDIR}/${PN}_${PV}"
-
src_prepare(){
# recent versions of htsjdk now use gradle,
# which is not supported by portage
@@ -37,8 +33,5 @@ src_compile(){
src_install(){
java-pkg_dojar *.jar lib/*.jar
- dodoc "${DISTDIR}"/${P}_UserManual.pdf \
- "${DISTDIR}"/${P}_Tutorial.txt \
- "${DISTDIR}"/${P}_QuickStart.txt \
- README.txt
+ einstalldocs
}
diff --git a/sci-biology/NGSEPcore/metadata.xml b/sci-biology/NGSEPcore/metadata.xml
index 642261079..6566fb214 100644
--- a/sci-biology/NGSEPcore/metadata.xml
+++ b/sci-biology/NGSEPcore/metadata.xml
@@ -11,5 +11,6 @@
</maintainer>
<upstream>
<remote-id type="sourceforge">ngsep</remote-id>
+ <remote-id type="github">NGSEP/NGSEPcore</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2021-03-24 12:36 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-03-24 12:36 UTC (permalink / raw
To: gentoo-commits
commit: 80e0be2e756675eda64a016d0d1b0f9b9eacdca9
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Mar 24 12:35:51 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Mar 24 12:35:51 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=80e0be2e
sci-biology/NGSEPcore: now really fix java.eclassesnotused
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
index ce80fc929..49b13a169 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit java-utils-2
+inherit java-pkg-2
DESCRIPTION="NGSEP (CNV and indel discovery)"
HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2021-03-24 12:26 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-03-24 12:26 UTC (permalink / raw
To: gentoo-commits
commit: b9199310d37a1bd8f3212d3a59e5a4b22eb24b5e
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Mar 24 12:25:12 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Mar 24 12:25:12 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9199310
sci-biology/NGSEPcore: fix java.eclassesnotused
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
index e001d175b..ce80fc929 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit java-pkg-2 java-ant-2
+inherit java-utils-2
DESCRIPTION="NGSEP (CNV and indel discovery)"
HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2021-01-10 12:27 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 12:27 UTC (permalink / raw
To: gentoo-commits
commit: 87260b125c1a2977523f2ebb99c364c7bcd8d86c
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 12:20:17 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 12:20:17 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87260b12
sci-biology/NGSEPcore: add version 4.0.3
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild | 44 ++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
new file mode 100644
index 000000000..7dc343127
--- /dev/null
+++ b/sci-biology/NGSEPcore/NGSEPcore-4.0.3.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+ https://github.com/NGSEP/NGSEPcore"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
+ https://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v${PV}.pdf -> ${P}_UserManual.pdf
+ https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
+ https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND=">=virtual/jdk-1.8"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+ # recent versions of htsjdk now use gradle,
+ # which is not supported by portage
+ #rm lib/htsjdk-2.22.jar || die
+ # TODO: package dev-java/jsci
+ #rm lib/jsci-core.jar || die
+ default
+}
+
+src_compile(){
+ emake -j1
+}
+
+src_install(){
+ java-pkg_dojar *.jar lib/*.jar
+ dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+ "${DISTDIR}"/${P}_Tutorial.txt \
+ "${DISTDIR}"/${P}_QuickStart.txt \
+ README.txt
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
@ 2019-03-27 16:24 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-27 16:24 UTC (permalink / raw
To: gentoo-commits
commit: 26f7eab8fcc5e6148f85e81a876d1362c28c8e4f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 27 16:23:05 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 27 16:23:05 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=26f7eab8
sci-biology/NGSEPcore: some improvements with the package
Still unfinished work.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 37 ++++++++++++++++++++++++++++
sci-biology/NGSEPcore/metadata.xml | 15 +++++++++++
2 files changed, 52 insertions(+)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
new file mode 100644
index 000000000..3f844bf16
--- /dev/null
+++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
+ https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf -> ${P}_UserManual.pdf
+ https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
+ https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-java/htsjdk"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+ rm -f *.jar lib/htsjdk-1.129.jar || die
+ default
+}
+
+src_compile(){
+ make -j1
+}
+
+src_install(){
+ java-pkg_dojar *.jar
+ dodoc "$DISTDIR}"/${P}_user_manual.pdf
+}
diff --git a/sci-biology/NGSEPcore/metadata.xml b/sci-biology/NGSEPcore/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+ <upstream>
+ <remote-id type="sourceforge">ngsep</remote-id>
+ </upstream>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
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