Initial import

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diff --git a/sci-biology/imagej/imagej-1.51k-r1.ebuild b/sci-biology/imagej/imagej-1.51k-r1.ebuild
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+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit java-pkg-2 java-ant-2 eutils versionator
+
+MY_PN="ij"
+MY_PV=$(delete_all_version_separators)
+
+# NOTE:
+# as plugins are regularly lagging behind, we use the pack released for previous
+# version instead. Change to present version locally if you are sure proper
+# version has been released.
+# see https://bugs.gentoo.org/show_bug.cgi?id=112275
+# https://github.com/imagej/imagej1/issues/28
+IJ_PV=$((${MY_PV::3}-1))
+
+DESCRIPTION="Image Processing and Analysis in Java"
+HOMEPAGE="http://rsb.info.nih.gov/ij/"
+
+SRC_URI="http://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip
+	http://rsb.info.nih.gov/ij/images/ImageJ.png
+	plugins? ( http://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )"
+# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins
+#	plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )"
+
+RESTRICT=""
+LICENSE="public-domain" # http://imagej.net/disclaimer.html
+SLOT="0"
+
+KEYWORDS=""
+
+IUSE="doc plugins debug"
+
+RDEPEND=">=virtual/jre-1.6:*
+	dev-java/java-config
+	dev-java/jython"
+DEPEND=">=virtual/jdk-1.6:*
+	dev-java/ant-core
+	${RDEPEND}"
+
+S=${WORKDIR}/source
+IJ_S=${WORKDIR}/ImageJ
+
+src_prepare() {
+	cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die
+
+	if ! use debug ; then
+		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
+	fi
+	epatch "${FILESDIR}"/AutoThresholder.java.patch
+	eapply_user
+}
+
+# in src_compile we get: !!! ERROR: Package jython was not found!
+# TODO: overwrite calls to jython ? See
+#   ij/plugin/frame/Editor.java
+#   plugin/PlugInInterpreter.java
+#   plugin/Macro_Runner.java
+
+src_compile() {
+	local antflags="build"
+	use doc && antflags="${antflags} javadocs"
+
+	ant ${antflags} || die  "ant build failed"
+
+	# Max memory usage depends on available memory and CPU type
+	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)
+	IJ_MAX_MEM=$(expr ${MEM} / 1024)
+	if use x86 && $IJ_MAX_MEM -gt 2048 ; then
+		IJ_MAX_MEM=2048
+	fi
+	# build finished, generate startup wrapper
+	cat <<EOF > "${T}/${PN}"
+#!${EPREFIX}/bin/bash
+IJ_LIB=${EPREFIX}/usr/share/${PN}/lib
+if !([ "\${IJ_HOME}" ]) ; then
+	IJ_HOME=\${HOME}/.imagej
+fi
+if [ -d \${IJ_HOME}/plugins ] ; then
+	IJ_PLG=\${IJ_HOME}
+else
+	IJ_PLG=${EPREFIX}/usr/share/${PN}/lib
+fi
+if !([ "\$IJ_MEM" ]) ; then
+	IJ_MEM=${IJ_MAX_MEM}
+fi
+if !([ "\$IJ_CP" ]) ; then
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar
+else
+	IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP}
+fi
+\$(java-config --java) \\
+	-Xmx\${IJ_MEM}m -Dswing.aatext=true \\
+	-Dawt.useSystemAAFontSettings=on\\
+	-cp \${IJ_CP} \\
+	-Duser.home=\${IJ_HOME} \\
+	-Dplugins.dir=\${IJ_PLG} \\
+	ij.ImageJ "\$@"
+EOF
+}
+
+src_install() {
+	java-pkg_dojar *.jar
+	dobin "${T}/${PN}"
+
+	if use plugins ; then
+		cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/
+		cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/
+	fi
+
+	use doc && java-pkg_dohtml -r "${WORKDIR}"/api
+
+	insinto /usr/share/pixmaps
+	doins "${WORKDIR}/${PN}".png
+	make_desktop_entry "${PN}" ImageJ "${PN}".png Graphics
+}
+
+pkg_postinst() {
+	einfo ""
+	einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt,"
+	einfo "by setting the environmental variable, \$IJ_HOME."
+	einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt."
+	einfo ""
+	einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM,"
+	einfo "and the class path by setting the environmental variable, \$IJ_CP."
+	einfo ""
+	einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html"
+	einfo "and add *.class files to \$IJ_HOME/plugins folder"
+	einfo ""
+}