sci-biology/micro-manager: udpate'
This commit is contained in:
Florian Tham
190
sci-biology/micro-manager/micro-manager-9999.ebuild
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190
sci-biology/micro-manager/micro-manager-9999.ebuild
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# Copyright 1999-2015 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: $
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EAPI=5
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PYTHON_COMPAT=( python{2_6,2_7,3_1,3_2,3_3,3_4} )
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DISTUTILS_OPTIONAL=1
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CONFIG_CHECK="VIDEO_V4L2"
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JAVA_ANT_DISABLE_ANT_CORE_DEP=1
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inherit autotools java-pkg-opt-2 java-ant-2 distutils-r1 linux-info vcs-snapshot
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MY_PN="micromanager-upstream"
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DESCRIPTION="The Open Source Microscopy Software"
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HOMEPAGE="http://www.micro-manager.org/"
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if [[ ${PV} == 9999 ]]; then
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inherit git-r3
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EGIT_REPO_URI="https://github.com/mdcurtis/${MY_PN}.git"
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SRC_URI=""
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else
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SRC_URI="http://github.com/mdcurtis/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
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fi
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SLOT="0"
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LICENSE="GPL-3 BSD LGPL-2.1"
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KEYWORDS="~amd64 ~x86"
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IUSE_proprietary="andor andorsdk3"
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IUSE="+X +java python doc ${IUSE_proprietary}"
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REQUIRED_USE="X? ( java ) python? ( ${PYTHON_REQUIRED_USE} )"
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CAMERA_DEPS="
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dev-libs/hidapi
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dev-libs/libusb-compat
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media-libs/freeimage
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media-libs/libdc1394
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media-libs/libgphoto2
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media-libs/opencv
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"
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PROPRIETARY_DEPS="
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andor? ( sci-libs/andor-camera-driver:2 )
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andorsdk3? ( sci-libs/andor-camera-driver:3 )
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"
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COMMON_DEPS="
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${CAMERA_DEPS}
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${PROPRIETARY_DEPS}
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X? (
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dev-java/commons-math:2
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dev-java/commons-math:3
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sci-libs/TSFProto:0
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sci-libs/bioformats:0
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dev-java/absolutelayout
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dev-java/bsh:0
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dev-java/gson:2.2.2
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dev-java/guava:17
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dev-java/jcommon:1.0
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dev-java/jfreechart:1.0
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dev-java/joda-time:0
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dev-java/miglayout:0
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dev-java/rsyntaxtextarea:0
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dev-java/swing-layout:1
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dev-java/swingx:1.6
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dev-lang/clojure:1.6
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dev-java/clojure-core-cache:0
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dev-java/clojure-core-memoize:0
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dev-java/clojure-data-json:0
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dev-libs/protobuf:0=[java]
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>=sci-biology/imagej-1.48:0=
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)
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python? ( dev-python/numpy[${PYTHON_USEDEP}] ${PYTHON_DEPS} )
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"
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RDEPEND="
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${COMMON_DEPS}
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java? ( >=virtual/jre-1.6 )
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"
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DEPEND="
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${COMMON_DEPS}
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dev-libs/boost
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doc? ( app-doc/doxygen )
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java? (
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>=virtual/jdk-1.6
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dev-lang/swig
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dev-java/ant-core
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>=dev-java/ant-contrib-1.0_beta3:0
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dev-java/hamcrest-core:1.3
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>=dev-java/junit-4.11:4
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)
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python? ( dev-lang/swig )
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"
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JAVA_ANT_REWRITE_CLASSPATH=1
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JAVA_ANT_CLASSPATH_TAGS="mm-javac javac xjavac"
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EANT_GENTOO_CLASSPATH="bsh,imagej,clojure-1.6,joda-time,bioformats,commons-math-2,commons-math-3,gson-2.2.2,guava-17,jcommon-1.0,jfreechart-1.0,miglayout,rsyntaxtextarea,swingx-1.6,TSFProto,protobuf"
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ECLJ_GENTOO_CLASSPATH="clojure-core-cache,clojure-core-memoize,clojure-data-json"
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pkg_setup() {
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java-pkg-opt-2_pkg_setup
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linux-info_pkg_setup
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}
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src_prepare() {
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epatch "${FILESDIR}"/secretdevice.patch
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epatch "${FILESDIR}"/drop_direct_junit_paths.patch
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epatch "${FILESDIR}"/disable_prefs_during_clojure_builds.patch
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epatch "${FILESDIR}"/makefile.am-typo.patch
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# Disable build of plugins that are impossible to satisfy the dependencies of
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local ech
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for ech in ClojureEditor ; do
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sed -i -e "/${ech}.jar/d" plugins/Makefile.am || die
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mv plugins/${ech}/build.xml{,.donotbuild} || die
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done
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eautoreconf
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java-pkg-opt-2_src_prepare
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use python && distutils-r1_src_prepare
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}
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src_configure() {
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local conf_opts my_ant_flags=()
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if use X ; then
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local ij_jar=$(java-pkg_getjar imagej ij.jar)
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local ij_dir=$(dirname ${ij_jar})
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else
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conf_opts+=" --disable-java-app"
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fi
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if use java ; then
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local jdk_home=$(java-config -O)
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# ./configure fails when it sees eselect-java's bash scripts.
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conf_opts+=" JAVA_HOME=${jdk_home}"
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conf_opts+=" JAVA=$(java-config -J)"
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conf_opts+=" JAVAC=$(java-config -c)"
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conf_opts+=" JAR=$(java-config -j)"
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my_ant_flags+=( -Dmm.build.java.lib.ant-contrib=$(java-pkg_getjar --build-only ant-contrib ant-contrib.jar) )
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my_ant_flags+=( -Dmm.build.java.lib.junit=$(java-pkg_getjar --build-only junit-4 junit.jar) )
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my_ant_flags+=( -Dmm.build.java.lib.hamcrest-core=$(java-pkg_getjar --build-only hamcrest-core-1.3 hamcrest-core.jar) )
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my_ant_flags+=( -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(java-pkg_getjars --with-dependencies ${ECLJ_GENTOO_CLASSPATH}) )
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fi
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if use python ; then
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python_setup
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local python_home=$(python_get_library_path)
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fi
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ANTFLAGS="${my_ant_flags[@]}" \
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CC="$(tc-getCC)" CXX="$(tc-getCXX)" LD="$(tc-getLD)" AR="$(tc-getAR)" RANLIB="$(tc-getRANLIB)" \
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econf \
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$(use_enable X imagej-plugin ${ij_dir}) \
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--disable-install-dependency-jars \
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$(use_with java java ${jdk_home}) \
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$(use_with python python ${python_home}) \
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$(use_with X ij-jar ${ij_jar}) \
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${conf_opts}
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java-ant-2_src_configure
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java-ant_rewrite-classpath buildscripts/javabuild.xml
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java-ant_rewrite-classpath autofocus/buildscripts/autofocusbuild.xml
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# manually hack gentoo.classpath into the clojure classpath
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sed -i -e 's#.*</clj-classpath>.*#<pathelement path="${gentoo.classpath}"/>\n&#' \
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buildscripts/clojurebuild.xml || die
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}
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src_install() {
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emake DESTDIR="${D}" install
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# TODO doc.
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# TODO source.
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# TODO examples.
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use java && java-pkg_regjar /usr/share/imagej/lib/plugins/Micro-Manager/{MMCoreJ,MMJ_,MMAcqEngine}.jar
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if use X; then
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java-pkg_dolauncher ${PN}-standalone \
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--main org.micromanager.MMStudio \
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--pwd /usr/share/imagej/lib \
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--java_args '-Xmx1024M -XX:MaxDirectMemorySize=1000G' \
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--pkg_args '-Dmmcorej.library.loading.stderr.log=yes -Dmmcorej.library.path="/usr/share/imagej/lib" -Dorg.micromanager.plugin.path="/usr/share/imagej/lib/mmplugins" -Dorg.micromanager.autofocus.path="/usr/share/imagej/lib/mmautofocus" -Dorg.micromanager.default.config.file="/usr/share/imagej/lib/MMConfig_demo.cfg" -Dorg.micromanager.corelog.dir=/tmp' \
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java-pkg_dolauncher ${PN} \
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--main ij.ImageJ \
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--pwd /usr/share/imagej/lib \
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--java_args '-Xmx1024M -XX:MaxDirectMemorySize=1000G' \
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--pkg_args '-Dmmcorej.library.loading.stderr.log=yes -Dmmcorej.library.path="/usr/share/imagej/lib" -Dorg.micromanager.plugin.path="/usr/share/imagej/lib/mmplugins" -Dorg.micromanager.autofocus.path="/usr/share/imagej/lib/mmautofocus" -Dorg.micromanager.default.config.file="/usr/share/imagej/lib/MMConfig_demo.cfg" -Dorg.micromanager.corelog.dir=/tmp' \
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make_desktop_entry "${PN} -eval 'run(\"Micro-Manager Studio\");'" "Micro-Manager Studio" ImageJ \
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"Graphics;Science;Biology"
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fi
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}
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