sci-biology/micro-manager: udpate'
This commit is contained in:
Florian Tham
203
sci-biology/micro-manager/micro-manager-1.4.13.ebuild
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203
sci-biology/micro-manager/micro-manager-1.4.13.ebuild
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# Copyright 1999-2014 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} )
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PYTHON_SINGLE_TARGET="python2_7"
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inherit eutils autotools python-single-r1 java-pkg-opt-2 flag-o-matic java-utils-2 linux-info vcs-snapshot
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MY_PN="micromanager-upstream"
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MY_P="${MY_PN}-${PV}"
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DESCRIPTION="The Open Source Microscopy Software"
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HOMEPAGE="http://www.micro-manager.org/"
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SRC_URI="http://github.com/mdcurtis/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
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SLOT="0"
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LICENSE="LGPL-2.1 BSD GPL-1 GPL-3"
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KEYWORDS="~x86 ~amd64"
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IUSE="+java python clojure_editor ieee1394 andor"
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RESTRICT="mirror"
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RDEPEND="java? (
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>=virtual/jre-1.5
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)
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ieee1394? ( media-libs/libdc1394 )"
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DEPEND="dev-lang/swig
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dev-libs/boost
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java? (
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>=virtual/jdk-1.5
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>=sci-biology/imagej-1.46e
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dev-java/bsh
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dev-java/commons-math:2
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dev-java/swingx:1.6
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dev-java/swing-layout:1
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dev-java/absolutelayout
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dev-java/jfreechart:1.0
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dev-lang/clojure
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clojure_editor? ( dev-util/clooj )
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sci-libs/TSFProto
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sci-libs/bioformats
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)
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python? (
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${PYTHON_DEPS}
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dev-python/numpy
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)
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andor? ( sci-libs/andor-camera-driver:2 )"
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pkg_setup() {
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if linux_config_exists; then
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linux_chkconfig_string VIDEO_V4L2
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if ! linux_chkconfig_present VIDEO_V4L2; then
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einfo "Enable MEDIA_CAMERA_SUPPORT in kernel to install v4l DeviceAdapter."
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fi
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else
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ewarn "Could not confirm that v4l is compiled in kernel, so video4linux"
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ewarn "DeviceAdapter may silently fail to compile."
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fi
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use java && java-pkg-opt-2_pkg_setup
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use python && python-single-r1_pkg_setup
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}
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src_prepare() {
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einfo "Patching zlib detection"
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for file in configure.in DeviceKit/configure.in; do
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sed -i -e "s/libz.a/libz.so/g" $file
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done
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epatch ${FILESDIR}/mmcorepy_setup_add_zlib.patch
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einfo "Patching v4l detection"
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sed -i -e "s/libv4l2.h/linux\/videodev2.h/g" DeviceAdapters/configure.in
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epatch ${FILESDIR}/andor_camera_detection.patch
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epatch ${FILESDIR}/arduino_detection.patch
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ebegin "Bootstrap started. This can take several minutes"
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sh mmUnixBuild.sh
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eend
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einfo "Patching to prevent imagej collision"
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sed -i -e '/cp $(IJJARPATH)/d' mmstudio/Makefile.am
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einfo "Patching to prevent scripts removal"
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sed -i -e '/rm -rf $(IJPATH)\/scripts.*$/d' scripts/Makefile.am
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if use python; then
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einfo "Patching numpy include directory"
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local numpy_sitedir
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numpy_includedir=$(python_get_sitedir)/numpy/core/include/numpy
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sed -i -e "/include_dirs/s~=.*~= \[\"${numpy_includedir}\"\]~" MMCorePy_wrap/setup.py
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einfo "Patching Python bindings to respect DESTDIR"
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sed -i -e 's: $(DEVICEADAPTERPATH): $(DESTDIR)\/$(DEVICEADAPTERPATH):' MMCorePy_wrap/Makefile.am
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fi
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if use java; then
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einfo "Patching to allow parallel compilations of plugins"
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# making and clearing a single `build' directory prevents
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# multiple plugins from being built simultaneously
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sed -i -e 's/build/build_$@/g' plugins/Makefile.am
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# TODO Make ebuilds for lwm, gaussian
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# Removing plugins requiring these deps until ebuilds made
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REMOVE_MM_PLUGINS="DataBrowser Gaussian"
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if ! use clojure_editor ; then
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REMOVE_MM_PLUGINS="${REMOVE_MM_PLUGINS} ClojureEditor"
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fi
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einfo "Removing unsupported Clojure plugins: ${REMOVE_MM_PLUGINS}"
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for PLUGIN in ${REMOVE_MM_PLUGINS}; do
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einfo "Removing ${PLUGIN} plugin"
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sed -i -e "/^all:/s/$PLUGIN\.jar//g" \
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-e "/^\tcp $PLUGIN\.jar/d" \
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plugins/Makefile.am
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done
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eautoconf
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# FIXME eautoreconf should replace eautoconf and
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# subversion_bootstrap lines, but dies because
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# ./Makefile.am searches for the non-existent
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# SecretDeviceAdapters directory
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#eautoreconf
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fi
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}
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src_configure() {
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if use java; then
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append-cppflags $(java-pkg_get-jni-cflags)
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IMAGEJ_DIR=$(dirname `java-pkg_getjar imagej ij.jar`) \
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ebegin 'Creating symlinks to .jar dependencies...'
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mkdir -p ../3rdpartypublic/classext/
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pushd ../3rdpartypublic/classext/
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java-pkg_jar-from bsh bsh.jar bsh-2.0b4.jar
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java-pkg_jar-from swingx-1.6 swingx.jar swingx-0.9.5.jar
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java-pkg_jar-from commons-math-2 commons-math.jar commons-math-2.0.jar
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java-pkg_jar-from swing-layout-1 swing-layout.jar swing-layout-1.0.4.jar
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java-pkg_jar-from absolutelayout absolutelayout.jar AbsoluteLayout.jar
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java-pkg_jar-from jfreechart-1.0 jfreechart.jar jfreechart-1.0.13.jar
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java-pkg_jar-from jcommon-1.0 jcommon.jar jcommon-1.0.16.jar
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java-pkg_jar-from imagej
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java-pkg_jar-from clojure-1.4
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if use clojure_editor; then
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java-pkg_jar-from clooj clooj-0.3.4-standalone.jar clooj.jar
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fi
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java-pkg_jar-from protobuf protobuf.jar gproto.jar
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java-pkg_jar-from TSFProto
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java-pkg_jar-from bioformats
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# TODO: Make these dep ebuilds and symlinks for plugins:
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# lwm, gaussian
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popd
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eend
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else
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IMAGEJ_DIR='no'
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fi
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econf \
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--with-imagej=${IMAGEJ_DIR} \
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$(use_enable python)
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}
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src_compile() {
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emake
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}
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src_install() {
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emake DESTDIR="${D}" install
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if use java; then
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# FIXME java-pkg_dolauncher should replace this bash script.
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# Problems encountered when attempting this were:
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# 1. dolauncher uses the same name for the launcher and
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# the package (gjl_package). What we want for this
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# package is:
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# /usr/bin/micro-manager
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# to contain:
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# gjl_package=imagej
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# 2. Fixing issue #1 above by editing the output file
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# creates unusual behavior with Micro-Manager, always
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# asking to select a dataset to open on startup.
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cat <<-EOF > "${T}"/${PN}
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#!/bin/bash
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(
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# MM plugins won't load without changing to this path
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cd /usr/share/imagej/lib
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\$(java-config --java) \\
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-mx1024m \\
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-cp \$(java-config -p imagej,libreadline-java) \\
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ij.ImageJ -run "Micro-Manager Studio"
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) 2>&1 | tee >(logger -t micro-manager) -
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exit 0
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EOF
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make_desktop_entry "${PN}" "Micro-Manager Studio" imagej \
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"Graphics;Science;Biology"
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dobin "${T}"/${PN}
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fi
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}
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