sci-biology/micro-manager: udpate'
This commit is contained in:
Florian Tham
177
sci-biology/micro-manager/micro-manager-1.4.10.ebuild
Executable file
177
sci-biology/micro-manager/micro-manager-1.4.10.ebuild
Executable file
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# Copyright 1999-2012 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=4
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inherit eutils subversion autotools java-pkg-opt-2 flag-o-matic java-utils-2
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DESCRIPTION="The Open Source Microscopy Software"
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HOMEPAGE="http://valelab.ucsf.edu/~MM/MMwiki/"
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ESVN_REPO_URI="https://valelab.ucsf.edu/svn/micromanager2/trunk"
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ESVN_BOOTSTRAP="mmUnixBuild.sh"
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ESVN_REVISION=9309
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SLOT="0"
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LICENSE="BSD"
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KEYWORDS="~amd64 ~x86"
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IUSE="+java clojure_editor ieee1394 andor"
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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[plugins]
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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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)
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andor? ( sci-libs/andor-camera-driver:2 )"
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src_unpack() {
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subversion_src_unpack
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}
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src_prepare() {
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# fix 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}/andor_camera_detection.patch
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subversion_bootstrap
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# ESVN_PATCHES won't apply after bootstrap, so must use epatches
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epatch ${FILESDIR}/boost_ipc_detail.patch
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einfo "Patching to prevent imagej removal"
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sed -i -e '/rm -rf/d' scripts/Makefile.am
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einfo "Patching to prevent imagej collision"
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sed -i -e '/cp $(IJJARPATH)/d' mmstudio/Makefile.am
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einfo "Patching Andor camera driver for return code debugging"
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sed -i -e '/end of kdb/a \
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\
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// macro for finding the source of unsuccessful return error code\
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#define CATCH(err) if (err != DRV_SUCCESS) { \\\
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LogMessage("Return code %u instead of DRV_SUCCESS at %s/%s:%d\\n", \\\
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err, __FILE__, __FUNCTION__, __LINE__); \\\
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return (int)ret; \\\
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}' DeviceAdapters/Andor/Andor.cpp
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sed -i -e
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if use java; then
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# making and clearing a single `build' directory prevents
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# multiple plugins from being built simultaneously
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sed -i -e 's/build/build_$@/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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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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# 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 --with-imagej=${IMAGEJ_DIR}
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}
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src_compile() {
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emake
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}
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src_install() {
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emake DESTDIR="${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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