[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: 560b7f632fd3e83014db80dd310bd6617d24088b
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 20 11:01:30 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 20 11:01:30 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=560b7f63
sci-biology/vague-bin: fix MultipleKeywordsLines
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 1 -
1 file changed, 1 deletion(-)
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index 50ea6ca72..79ed9fc48 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -11,7 +11,6 @@ HOMEPAGE="https://vicbioinformatics.com/software.vague.shtml;
if [ "$PV" == "" ]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague;
- KEYWORDS=""
else
SRC_URI="https://vicbioinformatics.com/vague-${PV}.tar.gz;
KEYWORDS="~amd64"
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: 3ad08b5d01c8f7fbf6455808fa35a9976992da8e
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Jan 18 12:57:18 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Jan 18 12:57:18 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ad08b5d
sci-biology/vague-bin: fix fetching, EAPI bump
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 17 ++---
1 file changed, 10 insertions(+), 7 deletions(-)
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index dc327b8d6..50ea6ca72 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -1,20 +1,19 @@
-# Copyright 1999-2019 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
-[ "$PV" == "" ] && inherit git-r3
-
DESCRIPTION="GUI for Velvet de novo assembler"
-HOMEPAGE="http://www.vicbioinformatics.com/software.vague.shtml;
+HOMEPAGE="https://vicbioinformatics.com/software.vague.shtml;
if [ "$PV" == "" ]; then
+ inherit git-r3
EGIT_REPO_URI="https://github.com/Victorian-Bioinformatics-Consortium/vague;
KEYWORDS=""
else
- SRC_URI="http://www.vicbioinformatics.com/vague-${PV}.tar.gz;
+ SRC_URI="https://vicbioinformatics.com/vague-${PV}.tar.gz;
KEYWORDS="~amd64"
fi
@@ -28,8 +27,12 @@ DEPEND=">=virtual/jdk-1.5:*"
S="${WORKDIR}"/vague-${PV}
+PATCHES=(
+ "${FILESDIR}"/vague.patch
+)
+
src_prepare(){
- epatch "${FILESDIR}"/vague.patch
+ default
sed -e "s#-jar /usr/share#-jar ${EPREFIX}/usr/share#" -i vague || die
}
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: 72457ca425a702a0640f6bddeef66d3985d03ea5
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Tue Apr 30 18:40:23 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Apr 30 18:40:23 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=72457ca4
sci-biology/vague-bin: drop DEPEND on velvetk
It is gone from the tree.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index bbb594948..dc327b8d6 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -23,8 +23,7 @@ SLOT="0"
RDEPEND="
>=virtual/jre-1.5:*
- sci-biology/velvet
- sci-biology/velvetk"
+ sci-biology/velvet"
DEPEND=">=virtual/jdk-1.5:*"
S="${WORKDIR}"/vague-${PV}
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: 6a5c3a9302f84e7c243da951dce272c1019cb742
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jan 19 15:55:30 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 19 15:55:30 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6a5c3a93
sci-biology/vague-bin: respect EPREFIX
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index 6c72d6ee4..bbb594948 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -31,6 +31,7 @@ S="${WORKDIR}"/vague-${PV}
src_prepare(){
epatch "${FILESDIR}"/vague.patch
+ sed -e "s#-jar /usr/share#-jar ${EPREFIX}/usr/share#" -i vague || die
}
src_install(){
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: a099a5a6fdaa381c25d71d293aab2951791e8cbb
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Wed Feb 18 13:48:15 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Wed Feb 18 13:48:15 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a099a5a6
sci-biology/vague-bin: fix SLOT operators
Package-Manager: portage-2.2.17
---
sci-biology/vague-bin/ChangeLog | 3 +++
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 9 +
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog
index fbb1f77..1982d25 100644
--- a/sci-biology/vague-bin/ChangeLog
+++ b/sci-biology/vague-bin/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher j...@gentoo.org vague-bin-1.0.5.ebuild:
+ sci-biology/vague-bin: fix SLOT operators
+
09 Feb 2015; Marius Brehler mar...@linux.sungazer.de epga-.ebuild:
Switch from git-2 to git-r3; Cleanup; Fix KEYWORDS
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index 11ef16b..b1d8d14 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -22,12 +22,13 @@ fi
LICENSE=GPL-2
SLOT=0
-DEPEND==virtual/jre-1.5
+RDEPEND=
+ =virtual/jre-1.5:*
sci-biology/velvet
sci-biology/velvetk
-RDEPEND=${DEPEND}
+DEPEND==virtual/jdk-1.5:*
-S=${WORKDIR}/vague-${PV}
+S=${WORKDIR}/vague-${PV}
src_prepare(){
epatch ${FILESDIR}/vague.patch
@@ -35,5 +36,5 @@ src_prepare(){
src_install(){
dobin vague
- java-pkg_dojar vague.jar || die
+ java-pkg_dojar vague.jar
}
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/
commit: 44a2983ea076940bf40ba0a595a37323e984e28f
Author: Marius Brehler marbre AT linux DOT sungazer DOT de
AuthorDate: Mon Feb 9 09:09:07 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Mon Feb 9 09:09:07 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=44a2983e
sci-biology/vague-bin-1.0.5: Switch from git-2 to git-r3; Cleanup; Fix KEYWORDS
---
sci-biology/vague-bin/ChangeLog | 3 +++
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 6 ++
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog
index 30734b2..fbb1f77 100644
--- a/sci-biology/vague-bin/ChangeLog
+++ b/sci-biology/vague-bin/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Feb 2015; Marius Brehler mar...@linux.sungazer.de epga-.ebuild:
+ Switch from git-2 to git-r3; Cleanup; Fix KEYWORDS
+
*vague-bin-1.0.5 (08 Jan 2015)
08 Jan 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz +files/vague.patch,
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index 479d88a..11ef16b 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit java-pkg-2
-[ $PV == ] inherit git-2
+[ $PV == ] inherit git-r3
DESCRIPTION=GUI for Velvet de novo assembler
HOMEPAGE=http://www.vicbioinformatics.com/software.vague.shtml;
@@ -15,14 +15,12 @@ if [ $PV == ]; then
EGIT_REPO_URI=https://github.com/Victorian-Bioinformatics-Consortium/vague;
KEYWORDS=
else
- SRC_URI=http://www.vicbioinformatics.com/vague-${PV}.tar.gz;
+ SRC_URI=http://www.vicbioinformatics.com/vague-${PV}.tar.gz;
KEYWORDS=~amd64
fi
LICENSE=GPL-2
SLOT=0
-KEYWORDS=~amd64
-IUSE=
DEPEND==virtual/jre-1.5
sci-biology/velvet
[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/, sci-biology/vague-bin/files/
commit: 90b414bd2d7195138343e5ea4d129c3e6b067a6e
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Jan 8 12:42:22 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Jan 8 12:42:22 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=90b414bd
sci-biology/vague-bin: new java binary package
Package-Manager: portage-2.2.7
---
sci-biology/vague-bin/ChangeLog | 9 ++
sci-biology/vague-bin/files/vague.patch | 8 ++
sci-biology/vague-bin/metadata.xml | 9 ++
sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 41
4 files changed, 67 insertions(+)
diff --git a/sci-biology/vague-bin/ChangeLog b/sci-biology/vague-bin/ChangeLog
new file mode 100644
index 000..30734b2
--- /dev/null
+++ b/sci-biology/vague-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/vague-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*vague-bin-1.0.5 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz +files/vague.patch,
+ +metadata.xml, +vague-bin-1.0.5.ebuild:
+ sci-biology/vague-bin: new java binary package
diff --git a/sci-biology/vague-bin/files/vague.patch
b/sci-biology/vague-bin/files/vague.patch
new file mode 100644
index 000..61f4c1a
--- /dev/null
+++ b/sci-biology/vague-bin/files/vague.patch
@@ -0,0 +1,8 @@
+--- vague.ori 2015-01-08 13:31:31.755604378 +0100
vague 2015-01-08 13:31:49.525604424 +0100
+@@ -1,4 +1,4 @@
+ echo Starting Vague, please wait...
+ export VAGUE_DIR=`dirname $0`
+ export PATH=$PATH:$VAGUE_DIR
+-java -Xmx3750m -jar `dirname $0`/vague.jar $*
++java -Xmx3750m -jar /usr/share/vague-bin/lib/vague.jar $*
diff --git a/sci-biology/vague-bin/metadata.xml
b/sci-biology/vague-bin/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/vague-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
+ herdsci-biology/herd
+ maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+ /maintainer
+/pkgmetadata
diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
new file mode 100644
index 000..479d88a
--- /dev/null
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+[ $PV == ] inherit git-2
+
+DESCRIPTION=GUI for Velvet de novo assembler
+HOMEPAGE=http://www.vicbioinformatics.com/software.vague.shtml;
+
+if [ $PV == ]; then
+
EGIT_REPO_URI=https://github.com/Victorian-Bioinformatics-Consortium/vague;
+ KEYWORDS=
+else
+ SRC_URI=http://www.vicbioinformatics.com/vague-${PV}.tar.gz;
+ KEYWORDS=~amd64
+fi
+
+LICENSE=GPL-2
+SLOT=0
+KEYWORDS=~amd64
+IUSE=
+
+DEPEND==virtual/jre-1.5
+ sci-biology/velvet
+ sci-biology/velvetk
+RDEPEND=${DEPEND}
+
+S=${WORKDIR}/vague-${PV}
+
+src_prepare(){
+ epatch ${FILESDIR}/vague.patch
+}
+
+src_install(){
+ dobin vague
+ java-pkg_dojar vague.jar || die
+}
