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# Maintainer: Stefan Seemayer <mail@semicolonsoftware.de>
pkgname=jalview
pkgver=2.10.5
pkgrel=1
pkgdesc="Bioinformatics Multiple Alignment Editor"
arch=(any)
url="http://www.jalview.org/"
license=('GPL3')
depends=(java-runtime)

####### Auto-generated using update_sources.sh
### <INJECT_HERE> ###

source=(
  'http://www.jalview.org/webstart/jalview.jar'
  'http://www.jalview.org/webstart/JGoogleAnalytics_0.3.jar'
  'http://www.jalview.org/webstart/Jmol-14.6.4_2016.10.26.jar'
  'http://www.jalview.org/webstart/VARNAv3-93.jar'
  'http://www.jalview.org/webstart/VAqua5-patch.jar'
  'http://www.jalview.org/webstart/activation.jar'
  'http://www.jalview.org/webstart/apache-mime4j-0.6.jar'
  'http://www.jalview.org/webstart/axis.jar'
  'http://www.jalview.org/webstart/biojava-core-4.1.0.jar'
  'http://www.jalview.org/webstart/biojava-ontology-4.1.0.jar'
  'http://www.jalview.org/webstart/castor-1.1-cycle-xml.jar'
  'http://www.jalview.org/webstart/commons-codec-1.3.jar'
  'http://www.jalview.org/webstart/commons-discovery.jar'
  'http://www.jalview.org/webstart/commons-logging-1.1.1.jar'
  'http://www.jalview.org/webstart/groovy-all-2.4.12-indy.jar'
  'http://www.jalview.org/webstart/htsjdk-1.133.jar'
  'http://www.jalview.org/webstart/httpclient-4.0.3.jar'
  'http://www.jalview.org/webstart/httpcore-4.0.1.jar'
  'http://www.jalview.org/webstart/httpmime-4.0.3.jar'
  'http://www.jalview.org/webstart/jabaws-min-client-2.2.0.jar'
  'http://www.jalview.org/webstart/jalview_jnlp_vm.jar'
  'http://www.jalview.org/webstart/java-json.jar'
  'http://www.jalview.org/webstart/jaxrpc.jar'
  'http://www.jalview.org/webstart/jdas-1.0.4.jar'
  'http://www.jalview.org/webstart/jersey-client-1.19.jar'
  'http://www.jalview.org/webstart/jersey-core-1.19.jar'
  'http://www.jalview.org/webstart/jersey-json-1.19.jar'
  'http://www.jalview.org/webstart/jetty-http-9.2.10.v20150310.jar'
  'http://www.jalview.org/webstart/jetty-io-9.2.10.v20150310.jar'
  'http://www.jalview.org/webstart/jetty-server-9.2.10.v20150310.jar'
  'http://www.jalview.org/webstart/jetty-util-9.2.10.v20150310.jar'
  'http://www.jalview.org/webstart/jfreesvg-2.1.jar'
  'http://www.jalview.org/webstart/jhall.jar'
  'http://www.jalview.org/webstart/json_simple-1.1.jar'
  'http://www.jalview.org/webstart/jsoup-1.8.1.jar'
  'http://www.jalview.org/webstart/jsr311-api-1.1.1.jar'
  'http://www.jalview.org/webstart/jswingreader-0.3.jar'
  'http://www.jalview.org/webstart/log4j-to-slf4j-2.0-rc2.jar'
  'http://www.jalview.org/webstart/mail.jar'
  'http://www.jalview.org/webstart/miglayout-4.0-swing.jar'
  'http://www.jalview.org/webstart/regex.jar'
  'http://www.jalview.org/webstart/saaj.jar'
  'http://www.jalview.org/webstart/servlet-api-3.1.jar'
  'http://www.jalview.org/webstart/slf4j-api-1.7.7.jar'
  'http://www.jalview.org/webstart/slf4j-log4j12-1.7.7.jar'
  'http://www.jalview.org/webstart/spring-core-3.0.5.RELEASE.jar'
  'http://www.jalview.org/webstart/spring-web-3.0.5.RELEASE.jar'
  'http://www.jalview.org/webstart/vamsas-client.jar'
  'http://www.jalview.org/webstart/wsdl4j.jar'
  'http://www.jalview.org/webstart/xercesImpl.jar'
  'http://www.jalview.org/webstart/xml-apis.jar'
  'logo.gif'
  'jalview'
  'jalview.desktop'
)

noextract=(
  'jalview.jar'
  'JGoogleAnalytics_0.3.jar'
  'Jmol-14.6.4_2016.10.26.jar'
  'VARNAv3-93.jar'
  'VAqua5-patch.jar'
  'activation.jar'
  'apache-mime4j-0.6.jar'
  'axis.jar'
  'biojava-core-4.1.0.jar'
  'biojava-ontology-4.1.0.jar'
  'castor-1.1-cycle-xml.jar'
  'commons-codec-1.3.jar'
  'commons-discovery.jar'
  'commons-logging-1.1.1.jar'
  'groovy-all-2.4.12-indy.jar'
  'htsjdk-1.133.jar'
  'httpclient-4.0.3.jar'
  'httpcore-4.0.1.jar'
  'httpmime-4.0.3.jar'
  'jabaws-min-client-2.2.0.jar'
  'jalview_jnlp_vm.jar'
  'java-json.jar'
  'jaxrpc.jar'
  'jdas-1.0.4.jar'
  'jersey-client-1.19.jar'
  'jersey-core-1.19.jar'
  'jersey-json-1.19.jar'
  'jetty-http-9.2.10.v20150310.jar'
  'jetty-io-9.2.10.v20150310.jar'
  'jetty-server-9.2.10.v20150310.jar'
  'jetty-util-9.2.10.v20150310.jar'
  'jfreesvg-2.1.jar'
  'jhall.jar'
  'json_simple-1.1.jar'
  'jsoup-1.8.1.jar'
  'jsr311-api-1.1.1.jar'
  'jswingreader-0.3.jar'
  'log4j-to-slf4j-2.0-rc2.jar'
  'mail.jar'
  'miglayout-4.0-swing.jar'
  'regex.jar'
  'saaj.jar'
  'servlet-api-3.1.jar'
  'slf4j-api-1.7.7.jar'
  'slf4j-log4j12-1.7.7.jar'
  'spring-core-3.0.5.RELEASE.jar'
  'spring-web-3.0.5.RELEASE.jar'
  'vamsas-client.jar'
  'wsdl4j.jar'
  'xercesImpl.jar'
  'xml-apis.jar'
)

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)

### </INJECT_HERE> ###

package() {
  cd "$srcdir/"

  # set up directory structure
  mkdir -p $pkgdir/usr/{share/{applications,pixmaps,java/$pkgname},bin}

  install -Dm644 *.jar $pkgdir/usr/share/java/$pkgname/
  install -Dm755 jalview $pkgdir/usr/bin/
  install -Dm644 logo.gif $pkgdir/usr/share/pixmaps/jalview.gif
  install -Dm644 jalview.desktop $pkgdir/usr/share/applications/
}

# vim:set ts=2 sw=2 et: