* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2014-03-23 19:28 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:28 UTC (permalink / raw
To: gentoo-commits
commit: cd8730525dbda2bed9f0d1c2502b472a5d876cfc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:27:10 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:27:10 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd873052
sci-biology/jtreeview: a skeleton for a new package, needs help from java team for sure
---
sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
new file mode 100644
index 0000000..f0a9904
--- /dev/null
+++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+S="${WORKDIR}"/TreeView-1.1.6r4-src
+
+DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
+HOMEPAGE="http://jtreeview.sourceforge.net/"
+SRC_URI="http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
+ http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"
+#http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="virtual/jdk"
+RDEPEND="${DEPEND}
+ virtual/jre"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2014-03-23 19:34 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:34 UTC (permalink / raw
To: gentoo-commits
commit: 5f6f55e99be6a039327174a7b571d63188efb85b
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:27:32 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:27:32 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f6f55e9
sci-biology/jtreeview: a skeleton for a new package, needs help from java team for sure
---
sci-biology/jtreeview/metadata.xml | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/jtreeview/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: ef47bb72f356772f03e6c2ba8abe79203519d48e
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:24:24 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:24:24 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ef47bb72
sci-biology/jtreeview: fix SLOT operators
Package-Manager: portage-2.2.17
---
sci-biology/jtreeview/ChangeLog | 6 ++++++
sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild | 9 +++++----
2 files changed, 11 insertions(+), 4 deletions(-)
diff --git a/sci-biology/jtreeview/ChangeLog b/sci-biology/jtreeview/ChangeLog
new file mode 100644
index 0000000..55f3e53
--- /dev/null
+++ b/sci-biology/jtreeview/ChangeLog
@@ -0,0 +1,6 @@
+# ChangeLog for sci-biology/jtreeview
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> jtreeview-1.1.6.4.ebuild:
+ sci-biology/jtreeview: fix SLOT operators
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
index f0a9904..d523c85 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -10,7 +10,8 @@ S="${WORKDIR}"/TreeView-1.1.6r4-src
DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
HOMEPAGE="http://jtreeview.sourceforge.net/"
-SRC_URI="http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
+SRC_URI="
+ http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
http://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz"
#http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
@@ -19,6 +20,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="virtual/jdk"
+DEPEND="virtual/jdk:*"
RDEPEND="${DEPEND}
- virtual/jre"
+ virtual/jre:*"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2017-02-18 19:44 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-02-18 19:44 UTC (permalink / raw
To: gentoo-commits
commit: e9900b4a2cdf333713fe88e1fec69cbb29b84978
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 19:44:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 19:44:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9900b4a
sci-biology/jtreeview: improve ebuild
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild | 26 +++++++++++++++++++++-----
1 file changed, 21 insertions(+), 5 deletions(-)
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
index 8baf45264..729fccde2 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
@@ -1,10 +1,11 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
-inherit java-pkg-2 java-ant-2
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit java-pkg-2 java-ant-2 eutils perl-module
S="${WORKDIR}"/TreeView-1.1.6r4-src
@@ -17,9 +18,24 @@ SRC_URI="
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # resulting java binary does not execute for me
IUSE=""
-DEPEND="virtual/jdk:*"
+DEPEND=">virtual/jdk-1.5:*"
RDEPEND="${DEPEND}
- virtual/jre:*"
+ >=virtual/jre-1.5:*"
+
+# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
+
+src_install(){
+ java-pkg_dojar TreeView.jar
+ java-pkg_dolauncher ${PN} TreeView.jar
+ cd ../helper-scripts-0.0.2 || die
+ perl_set_version
+ insinto "${VENDOR_LIB}"
+ doins *.pm
+ dobin *.pl
+ insinto /usr/share/"${PN}"/examples
+ doins blues.color
+ newdoc README README.helper-scripts
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2017-02-18 20:02 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-02-18 20:02 UTC (permalink / raw
To: gentoo-commits
commit: 42e85b529ad724771b5879bf06678c338865329f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 20:02:45 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 20:02:45 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=42e85b52
sci-biology/jtreeview: add deemed dependency on nanoxml
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
index 729fccde2..d3c106ee9 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
@@ -21,7 +21,8 @@ SLOT="0"
KEYWORDS="" # resulting java binary does not execute for me
IUSE=""
-DEPEND=">virtual/jdk-1.5:*"
+DEPEND=">virtual/jdk-1.5:*
+ dev-java/nanoxml"
RDEPEND="${DEPEND}
>=virtual/jre-1.5:*"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2017-02-18 20:22 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-02-18 20:22 UTC (permalink / raw
To: gentoo-commits
commit: 1326710c5da26210005f4ec496b0c0a1af917077
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 20:22:12 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 20:22:12 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1326710c
sci-biology/jtreeview: add 3.0_alpha version which executes fine
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/jtreeview/jtreeview-9999.ebuild | 40 +++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
new file mode 100644
index 000000000..24c5427ae
--- /dev/null
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit java-pkg-2 git-r3
+
+DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
+HOMEPAGE="http://jtreeview.sourceforge.net
+ https://bitbucket.org/TreeView3Dev/treeview3"
+EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="" # builds and executes fines
+IUSE=""
+
+DEPEND=">virtual/jdk-1.7:*"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+src_prepare(){
+ chmod u+x ./gradle* || die
+ eapply_user
+}
+
+src_compile(){
+ # work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
+ # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+ # make jure SDK-1.8 is available, JRE-1.8 is not enough
+ GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
+}
+
+src_install(){
+ cd build/libs || die
+ java-pkg_dojar *.jar
+ java-pkg_dolauncher ${PN}
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2017-02-18 20:23 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-02-18 20:23 UTC (permalink / raw
To: gentoo-commits
commit: 88e003594469a266f9bb7a3d294d46b2b159fe27
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Feb 18 20:23:17 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Feb 18 20:23:17 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=88e00359
sci-biology/jtreeview: remove forgotten reference to perl
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/jtreeview/jtreeview-9999.ebuild | 1 -
1 file changed, 1 deletion(-)
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
index 24c5427ae..8ec30fc71 100644
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -4,7 +4,6 @@
EAPI=6
-PERL_EXPORT_PHASE_FUNCTIONS=no
inherit java-pkg-2 git-r3
DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: bcafdb1d945ea006828162f70d08f31f7d788a29
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:43:18 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:43:18 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bcafdb1d
sci-biology/jtreeview: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/jtreeview/jtreeview-9999.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
index 0b95e7cb3..316368b4e 100644
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -22,9 +22,8 @@ src_install(){
java-pkg_dolauncher ${PN} TreeView.jar
cd ../helper-scripts-0.0.2 || die
perl_set_version
- insinto "${VENDOR_LIB}"
- doins *.pm
- dobin *.pl
+ perl_domodule *.pm
+ perl_domodule *.pl
insinto /usr/share/"${PN}"/examples
doins blues.color
newdoc README README.helper-scripts
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/jtreeview/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: cf088e81e371c260b25f6e6fd5448cc9f0441e8c
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:44:17 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:44:17 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf088e81
sci-biology/jtreeview: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/jtreeview/jtreeview-1.2.0.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
index 34a6ae178..8f0e777c9 100644
--- a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
@@ -31,9 +31,8 @@ src_install(){
java-pkg_dolauncher ${PN} TreeView.jar
cd ../helper-scripts-0.0.2 || die
perl_set_version
- insinto "${VENDOR_LIB}"
- doins *.pm
- dobin *.pl
+ perl_domodule *.pm
+ perl_domodule *.pl
insinto /usr/share/"${PN}"/examples
doins blues.color
newdoc README README.helper-scripts
^ permalink raw reply related [flat|nested] 9+ messages in thread
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