* [gentoo-commits] proj/sci:master commit in: sci-biology/conrad/
@ 2016-05-03 19:02 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-05-03 19:02 UTC (permalink / raw
To: gentoo-commits
commit: 53b862b685eda906c6becbbc09b10521a0919e57
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 3 19:01:51 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 3 19:01:51 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=53b862b6
sci-biology/conrad: new package, needs java spring
Package-Manager: portage-2.2.28
sci-biology/conrad/conrad-1.ebuild | 51 ++++++++++++++++++++++++++++++++++++++
sci-biology/conrad/metadata.xml | 12 +++++++++
2 files changed, 63 insertions(+)
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
new file mode 100644
index 0000000..f9e19a1
--- /dev/null
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Gene predictor using ab initio and ad hoc evidence (RNA-Seq, BLAST) on gDNA"
+HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
+ http://sourceforge.net/projects/conradcrf"
+SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="
+ >=virtual/jre-1.5:*
+ dev-java/commons-logging
+ >=dev-java/commons-lang-2.1:*
+ dev-java/colt
+ dev-java/dom4j
+ "
+ # spring # see bug #97004
+ # LBFGS
+DEPEND="${RDEPEND}
+ >=virtual/jdk-1.5:*
+ dev-java/ant-core
+ >=dev-java/jfreechart-1.0.3
+ >=dev-java/jcommon-1.0.6
+ >=dev-java/commons-math-1.1
+ "
+S="${WORKDIR}"
+
+src_prepare(){
+ sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
+}
+
+src_compile(){
+ cd dev || die
+ ant compile || die
+}
+
+src_install() {
+ dobin bin/conrad.sh
+ java-pkg_dojar lib/conrad.jar
+ insinto /usr/share/conrad
+ dodoc -r docs models samples trainingFiles
+}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/conrad/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] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/conrad/
@ 2016-07-12 16:18 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-07-12 16:18 UTC (permalink / raw
To: gentoo-commits
commit: 3a228937d5822bfdefd17539f8089eac13f427ef
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:16:10 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:16:10 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a228937
sci-biology/conrad: document more issues with the ebuild
Package-Manager: portage-2.2.28
sci-biology/conrad/conrad-1.ebuild | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
index f9e19a1..983be76 100644
--- a/sci-biology/conrad/conrad-1.ebuild
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2 java-ant-2
-DESCRIPTION="Gene predictor using ab initio and ad hoc evidence (RNA-Seq, BLAST) on gDNA"
+DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor"
HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
http://sourceforge.net/projects/conradcrf"
SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
@@ -16,17 +16,20 @@ SLOT="0"
KEYWORDS=""
IUSE=""
+# upstream binaries do not work with oracle-java-8
RDEPEND="
>=virtual/jre-1.5:*
+ <=virtual/jre-1.7:*
dev-java/commons-logging
>=dev-java/commons-lang-2.1:*
dev-java/colt
dev-java/dom4j
"
# spring # see bug #97004
- # LBFGS
+ # dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
DEPEND="${RDEPEND}
>=virtual/jdk-1.5:*
+ <=virtual/jdk-1.7:*
dev-java/ant-core
>=dev-java/jfreechart-1.0.3
>=dev-java/jcommon-1.0.6
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/conrad/
@ 2016-12-13 6:59 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2016-12-13 6:59 UTC (permalink / raw
To: gentoo-commits
commit: d1b5ff759d3e3b01e9d5a2d8fcfd1cfb44345915
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec 13 06:56:01 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec 13 06:56:01 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d1b5ff75
sci-biology/conrad: install startup file for a jar file
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/conrad/conrad-1.ebuild | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
index 983be76..10f73bb 100644
--- a/sci-biology/conrad/conrad-1.ebuild
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -48,7 +48,9 @@ src_compile(){
src_install() {
dobin bin/conrad.sh
+ java-pkg_newjar lib/conrad.jar
java-pkg_dojar lib/conrad.jar
+ java-pkg_dolauncher conrad --jar conrad.jar
insinto /usr/share/conrad
dodoc -r docs models samples trainingFiles
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/conrad/
@ 2021-01-05 18:56 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:56 UTC (permalink / raw
To: gentoo-commits
commit: 7551503c25287bff9b02c956f660adf647ec4c87
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 18:56:14 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:56:14 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7551503c
sci-biology/conrad: works just fine with jdk-1.8
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/conrad/conrad-1.ebuild | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
index 66acb381f..2185a23dd 100644
--- a/sci-biology/conrad/conrad-1.ebuild
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit java-pkg-2 java-ant-2
@@ -11,13 +11,11 @@ SRC_URI="https://downloads.sourceforge.net/project/conradcrf/conradcrf/Version%2
LICENSE="LGPL-2.1"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
-# upstream binaries do not work with oracle-java-8
RDEPEND="
>=virtual/jre-1.5:*
- <=virtual/jre-1.7:*
+ <virtual/jdk-1.9:*
dev-java/commons-logging
>=dev-java/commons-lang-2.1:*
dev-java/colt
@@ -27,7 +25,7 @@ RDEPEND="
# dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
DEPEND="${RDEPEND}
>=virtual/jdk-1.5:*
- <=virtual/jdk-1.7:*
+ <virtual/jdk-1.9:*
dev-java/ant-core
>=dev-java/jfreechart-1.0.3
>=dev-java/jcommon-1.0.6
@@ -36,6 +34,7 @@ DEPEND="${RDEPEND}
S="${WORKDIR}"
src_prepare(){
+ default
sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
}
@@ -46,9 +45,7 @@ src_compile(){
src_install() {
dobin bin/conrad.sh
- java-pkg_newjar lib/conrad.jar
java-pkg_dojar lib/conrad.jar
java-pkg_dolauncher conrad --jar conrad.jar
- insinto /usr/share/conrad
dodoc -r docs models samples trainingFiles
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/conrad/
@ 2021-01-19 16:26 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:26 UTC (permalink / raw
To: gentoo-commits
commit: fefdd2716525dee8dacf42e5881948fd1d8435fe
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:17:32 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:17:32 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fefdd271
sci-biology/conrad: depend on unzip
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/conrad/conrad-1.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
index 2185a23dd..bca495174 100644
--- a/sci-biology/conrad/conrad-1.ebuild
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -31,6 +31,7 @@ DEPEND="${RDEPEND}
>=dev-java/jcommon-1.0.6
>=dev-java/commons-math-1.1
"
+BDEPEND="app-arch/unzip"
S="${WORKDIR}"
src_prepare(){
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