Current Fiji PKGBUILDs from AUR

.SRCINFO

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+pkgbase = fiji-binary-latest
+	pkgdesc = ImageJ distribution with a lot of plugins for scientific (especially biology related) image processing.
+	pkgver = 20131123
+	pkgrel = 5
+	url = http://fiji.sc/
+	arch = i686
+	arch = x86_64
+	license = GPL
+	depends = java-runtime>=6
+	optdepends = java3d: For the 3D viewer plugin.
+	provides = fiji=20131123
+	provides = fiji-binary=20131123
+	conflicts = fiji-binary
+	replaces = fiji<=20131123
+	replaces = fiji-binary<=20131123
+	source = http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip
+	source = fiji.desktop
+	md5sums = SKIP
+	md5sums = 4c59f5f24368b179aab17eac1e1dfd2a
+
+pkgname = fiji-binary-latest
+

PKGBUILD

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+# Maintainer: radioxoma
+# Contributor: dreieck
+
+pkgname="fiji-binary-latest"
+pkgver=20131123
+pkgrel="5"
+pkgdesc="ImageJ distribution with a lot of plugins for scientific (especially biology related) image processing."
+arch=('i686' 'x86_64')
+url='http://fiji.sc/'
+license=('GPL')
+_licenses_plugins=('GPL' 'AL' 'SPL' 'LGPL' 'EPL' 'GPL2' 'PD' 'BIG' 'imagescience' 'BSD' 'AGPL' 'MPL1.1' 'CPL' 'PSF2' 'JSF2.1' 'JPSL' 'BSD-like' 'CPL1.0' 'BSDR' 'Citationware') ## Each component has it's individual license, but the AUR does not allow such a big license array ("Error - Package license cannot be greater than 40 characters"), so they are listed in this variable just for information purposes. (The PKGBUILD does not deal with that variable at all.)
+depends=('java-runtime>=6')
+optdepends=('java3d: For the 3D viewer plugin.')
+provides=("fiji=${pkgver}" "fiji-binary=${pkgver}")
+replaces=("fiji<=${pkgver}" "fiji-binary<=${pkgver}")
+conflicts=("fiji-binary")
+source=(
+        # "http://fiji.sc/downloads/Life-Line/fiji-nojre-${pkgver}.zip"
+        "http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip" ## This one is the "continuous build".
+        "fiji.desktop"
+       )
+md5sums=(
+         'SKIP'
+         '4c59f5f24368b179aab17eac1e1dfd2a'
+        )
+
+pkgver()
+{
+  echo "$(date +%Y%m%d)"
+}
+
+_userexecutable="fiji" # That name to be presented to the user.
+
+_executablebase="ImageJ-linux"
+if test "$CARCH" == "x86_64"; then
+  _executable="${_executablebase}64"
+else
+  _executable="${_executablebase}"
+fi
+
+build()
+{
+  _extractdir="${srcdir}/Fiji.app"
+
+  cd "${_extractdir}" || exit 11
+  _removefrompackage=('Contents' 'ImageJ-linux32' 'ImageJ-linux64' 'ImageJ-win32.exe' 'ImageJ-win64.exe') # Remove executables not suiting our architecture, and an ampty dir.
+  _executablebak="$(mktemp)" || exit 21 # Save the executable matching our architecture.
+  cp "${_executable}" "${_executablebak}" || exit 31
+  rm -Rf "${_removefrompackage[@]}" || exit 41
+  mv "${_executablebak}" "${_executable}" || exit 51
+  chmod a+x "${_executable}" || exit 56
+  ln -sf "${_executable}" "${_userexecutable}" || exit 61
+
+  # Associate fiji.desktop with appropriate binary
+  sed -ie "s/Exec=.*$/Exec=${_executable} %F/g" "${srcdir}/fiji.desktop"
+}
+
+package()
+{
+  _extractdir="${srcdir}/Fiji.app"
+
+  _targetdirinrootfs="/opt/fiji"
+  _targetdir="${pkgdir}/${_targetdirinrootfs}"
+  _bindir="${pkgdir}/usr/bin"
+  mkdir -p "${_targetdir}" || exit 111
+  mkdir -p "${_bindir}" || exit 116
+  cp -afv "${_extractdir}"/* "${_targetdir}" || exit 121
+  chown -R root:root "${_targetdir}" || true
+  cd "${_bindir}" || exit 125
+  # ln -sf "${_targetdir}/${_userexecutable}" "${_bindir}/${_userexecutable}" || exit 131 # We do NOT create a executable "fiji" in the PATH, since one may want to create a custum /usr/local/bin/fiji for setting JAVA_HOME to the SUN/Oracle java. Instead, we name the executable associated with the architecture, and have "fiji" in the /opt-dir.
+  ln -sf "${_targetdirinrootfs}/${_executable}" "${_executable}" || exit 135
+  install -Dm644 "${srcdir}/fiji.desktop" "${pkgdir}/usr/share/applications/fiji.desktop"
+}

fiji.desktop

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+[Desktop Entry]
+Type=Application
+Name=Fiji
+GenericName=Fiji Is Just ImageJ
+Comment=Image processing and analysis
+Categories=Graphics;Science;ImageProcessing;Biology;
+Icon=/opt/fiji/images/icon.png
+Exec='ImageJ-linux %f'