commit: 395c7e7490baf0d7a6e6550fd47d966c285dc171 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 15 21:38:28 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 15 21:38:28 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=395c7e74
sci-biology/imagej: new package Ebuild taken over from https://bugs.gentoo.org/show_bug.cgi?id=112275 src_compile screams about: >>> Compiling source in >>> /scratch/var/tmp/portage/sci-biology/imagej-1.51k/work/source ... !!! ERROR: Package jython was not found! but it builds fine using Apache ant. ImageJ2 is using maven as a build system ( https://imagej.net/ImageJ2 ) Package-Manager: Portage-2.3.3, Repoman-2.3.1 .../imagej/files/AutoThresholder.java.patch | 10 ++ sci-biology/imagej/imagej-1.51k.ebuild | 132 +++++++++++++++++++++ sci-biology/imagej/metadata.xml | 15 +++ 3 files changed, 157 insertions(+) diff --git a/sci-biology/imagej/files/AutoThresholder.java.patch b/sci-biology/imagej/files/AutoThresholder.java.patch new file mode 100644 index 000000000..97c893244 --- /dev/null +++ b/sci-biology/imagej/files/AutoThresholder.java.patch @@ -0,0 +1,10 @@ +--- imagej-1.51k/work/source/ij/process/AutoThresholder.java.ori 2017-03-15 22:33:45.843801175 +0100 ++++ imagej-1.51k/work/source/ij/process/AutoThresholder.java 2017-03-15 22:33:55.104053480 +0100 +@@ -650,7 +650,6 @@ + } + // The threshold is the minimum between the two peaks. + for (int i=1; i<255; i++) { +- //IJ.log(" "+i+" "+iHisto[i]); + if (iHisto[i-1] > iHisto[i] && iHisto[i+1] >= iHisto[i]) { + threshold = i; + break; diff --git a/sci-biology/imagej/imagej-1.51k.ebuild b/sci-biology/imagej/imagej-1.51k.ebuild new file mode 100644 index 000000000..0467973e4 --- /dev/null +++ b/sci-biology/imagej/imagej-1.51k.ebuild @@ -0,0 +1,132 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=6 + +inherit java-pkg-2 java-ant-2 eutils versionator + +MY_PN="ij" +MY_PV=$(delete_all_version_separators) + +# NOTE: +# as plugins are regularly lagging behind, we use the pack released for previous +# version instead. Change to present version locally if you are sure proper +# version has been released. +# see https://bugs.gentoo.org/show_bug.cgi?id=112275 +IJ_PV=$(expr ${MY_PV::3} - 1) + +DESCRIPTION="Image Processing and Analysis in Java" +HOMEPAGE="http://rsb.info.nih.gov/ij/"; + +SRC_URI="http://imagej.nih.gov/ij/download/src/${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" +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 ${EPREFIX}/proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) + IJ_MAX_MEM=$(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} +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}, i.e. \${HOME}/plugins and \${HOME}/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 "" +} diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml new file mode 100644 index 000000000..4f14b2e58 --- /dev/null +++ b/sci-biology/imagej/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="plugins">Install additional plugins</flag> + </use> +</pkgmetadata>
