commit: 26212fea17cb62e4fc20bb50e26d47e63c511b0d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:54:55 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:55:06 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=26212fea
sci-biology/jtreeview: fix fetch, fix build, EAPI bump
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
...eview-1.1.6.4.ebuild => jtreeview-1.2.0.ebuild} | 25 +++++++--------
sci-biology/jtreeview/jtreeview-9999.ebuild | 37 +++++++++-------------
3 files changed, 27 insertions(+), 36 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index b6e454b48..31c424659 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -72,4 +72,3 @@ sci-biology/hydra-sv
sci-biology/ICC
sci-biology/IMAGE
sci-biology/jannovar
-sci-biology/jtreeview
diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
similarity index 57%
rename from sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
rename to sci-biology/jtreeview/jtreeview-1.2.0.ebuild
index e89e14cf0..34a6ae178 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
@@ -1,29 +1,28 @@
-# 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
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit java-pkg-2 java-ant-2 eutils perl-module
-
-S="${WORKDIR}"/TreeView-1.1.6r4-src
+inherit perl-module java-pkg-2 java-ant-2
DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
HOMEPAGE="http://jtreeview.sourceforge.net/"; # no https
SRC_URI="
-
https://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-src.tar.gz
-
https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz";
-#http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.6r4/TreeView-1.1.6r4-bin.tar.gz
+
https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-src.tar.gz
+
https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
+"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="" # resulting java binary does not execute for me
-IUSE=""
+KEYWORDS="~amd64"
-DEPEND=">virtual/jdk-1.5:*
+DEPEND=">virtual/jdk-1.7:*
dev-java/nanoxml"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5:*"
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}/TreeView-${PV}-src"
+JAVA_PKG_BSFIX_NAME="${S}"
# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild
b/sci-biology/jtreeview/jtreeview-9999.ebuild
index 159448ab7..0b95e7cb3 100644
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -1,38 +1,31 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit java-pkg-2 git-r3
+inherit perl-module java-pkg-2 java-ant-2 git-r3
DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net
- https://bitbucket.org/TreeView3Dev/treeview3"; # no https
+HOMEPAGE="http://jtreeview.sourceforge.net/"; # no https
EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git";
LICENSE="MIT"
SLOT="0"
-KEYWORDS="" # builds and executes fines
-IUSE=""
+KEYWORDS=""
DEPEND=">virtual/jdk-1.7:*"
RDEPEND="${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}
+ 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
}
