mirror of
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artemis: build from source prepare
This commit is contained in:
Kuoi
parent
d133fe9751
commit
1850076697
8 changed files with 522 additions and 0 deletions
75
prepare/artemis/PKGBUILD
Normal file
75
prepare/artemis/PKGBUILD
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@ -0,0 +1,75 @@
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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
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# Contributor: Clint Valentine <valentine.clint@gmail.com>
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pkgname=artemis
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_pkgname=Artemis
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pkgver=18.2.0
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pkgrel=5
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pkgdesc='A genome viewer and annotation tool that visualizes biological sequence features'
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arch=('x86_64')
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url=https://www.sanger.ac.uk/science/tools/"${pkgname}"
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license=('GPL2')
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depends=('java-runtime')
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makedepends=('java-environment' 'maven')
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source=($pkgname-$pkgver.tar.gz::https://github.com/sanger-pathogens/Artemis/archive/refs/tags/v${pkgver}.tar.gz
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act.desktop
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artemis.desktop
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bamview.desktop
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dnaplotter.desktop)
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sha256sums=('842c055f5cce021adbaea4f076b2ea80335ab1e44fbaa34b2ab608df6314a18e'
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'a7dda77f6518c98af6df88ba5d725f1b89d86aca125240f63a9c6e08afeb2a24'
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'dea9a1cc47b110c4f6ebe17c1b698866082997ffd9e6008d89847ddf745a0789'
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'3ca519b00ffac02d635a62884996ad5b8c4580d8ffe8fcd427ee4edee1562f00'
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'ef584b45f9c92da15511779f20a1a1449915315066662e4c142ea4cd92dd717c')
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#prepare() {
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#scripts=('act' 'art' 'bamview' 'dnaplotter')
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# cd $srcdir/$_pkgname-$pkgver
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# patch -N -i $srcdir/fix_bin.patch
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#}
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build() {
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cd $srcdir/$_pkgname-$pkgver
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mvn validate
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mvn package
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}
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package() {
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bina=('act' 'art' 'bamview' 'dnaplotter')
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scripts=('act' 'artemis' 'bamview' 'dnaplotter')
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# desktop
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cd $srcdir/
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for des in ${scripts[@]}
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do
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install -Dm 755 $des.desktop $pkgdir/usr/share/applications/$des.desktop
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done
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# bin
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cd $srcdir/$_pkgname-$pkgver
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for bin in ${bina[@]}
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do
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install -Dm 775 $bin $pkgdir/usr/share/$pkgname/$bin
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done
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# jar
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cd $srcdir/$_pkgname-$pkgver/target/jars
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for jar in $(ls *.jar)
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do
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install -Dm 755 $jar $pkgdir/usr/share/$pkgname/target/jars/$jar
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done
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# icons
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cd $srcdir/$_pkgname-$pkgver/target/classes/images
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for icn in ${scripts[@]}
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do
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mv ${icn}_icon.png ${icn}.png
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install -Dm 644 ${icn}.png $pkgdir/usr/share/pixmaps/${icn}.png
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done
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# link bin
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cd $srcdir/$_pkgname-$pkgver
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mkdir -p $pkgdir/usr/bin
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for bin in ${bina[@]}
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do
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ln -s /usr/share/$pkgname/$bin $pkgdir/usr/bin/$bin
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done
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}
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16
prepare/artemis/act.desktop
Executable file
16
prepare/artemis/act.desktop
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[Desktop Entry]
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Categories=
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Encoding=UTF-8
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Exec=act
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GenericName=
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Icon=act
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MimeType=
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Name=act
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ServiceTypes=
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SwallowExec=
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SwallowTitle=
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Terminal=false
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TerminalOptions=
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Type=Application
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X-KDE-SubstituteUID=false
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X-KDE-Username=root
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16
prepare/artemis/artemis.desktop
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16
prepare/artemis/artemis.desktop
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[Desktop Entry]
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Categories=
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Encoding=UTF-8
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Exec=art
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GenericName=
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Icon=artemis
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MimeType=
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Name=artemis
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ServiceTypes=
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SwallowExec=
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SwallowTitle=
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Terminal=false
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TerminalOptions=
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Type=Application
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X-KDE-SubstituteUID=false
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X-KDE-Username=root
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16
prepare/artemis/bamview.desktop
Executable file
16
prepare/artemis/bamview.desktop
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@ -0,0 +1,16 @@
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[Desktop Entry]
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Categories=
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Encoding=UTF-8
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Exec=bamview
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GenericName=
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Icon=bamview
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MimeType=
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Name=bamview
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ServiceTypes=
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SwallowExec=
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SwallowTitle=
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Terminal=false
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TerminalOptions=
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Type=Application
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X-KDE-SubstituteUID=false
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X-KDE-Username=root
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16
prepare/artemis/dnaplotter.desktop
Executable file
16
prepare/artemis/dnaplotter.desktop
Executable file
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[Desktop Entry]
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Categories=
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Encoding=UTF-8
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Exec=dnaplotter
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GenericName=
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Icon=dnaplotter
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MimeType=
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Name=dnaplotter
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ServiceTypes=
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SwallowExec=
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SwallowTitle=
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Terminal=false
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TerminalOptions=
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Type=Application
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X-KDE-SubstituteUID=false
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X-KDE-Username=root
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362
prepare/artemis/fix_bin.patch
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362
prepare/artemis/fix_bin.patch
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@ -0,0 +1,362 @@
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Description: Simplifying the provided launchers
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Many options or tricks are useless on a Debian system.
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The paths are also adapted to the Debian install.
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Author: Pierre Gruet <pgt@debian.org>
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Forwarded: not-needed
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Last-Update: 2020-09-06
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--- a/act
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+++ b/act
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@@ -38,36 +38,6 @@
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exit 0
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}
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-add_proxy_properties() {
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_PROXY
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- fi
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_proxy
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- fi
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-
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- if [[ "$http_proxy" != "" ]]
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- then
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- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
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- fi
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-}
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-
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-#
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-# Resolve script path (inc symlinks)
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-#
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-SOURCE="${BASH_SOURCE[0]}"
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-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
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- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
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- SOURCE="$(readlink "$SOURCE")"
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- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
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-done
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-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
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-
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-
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# Special Sanger override on chado PGUSER
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if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
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then
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@@ -93,28 +63,6 @@
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shift
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done
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-
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-JAR_NAME=act.jar
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-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
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-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
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-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
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-
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-#
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-# Use a custom Java version if necessary
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-#
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-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
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-then
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- JAVA=`which java`
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-else
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- JAVA_HOME=$ARTEMIS_JAVA_JRE
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- JAVA=$ARTEMIS_JAVA_JRE/bin/java
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-fi
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-
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-#
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-# Allow URLs to work from behind firewalls.
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-#
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-add_proxy_properties
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-
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#
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# "-mx2g" sets the maximum amount of memory to use.
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# This may need to be increased when dealing with large files
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@@ -132,20 +80,12 @@
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#
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FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
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-PLATTMP=`uname`
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-if [[ "$PLATTMP" = "Darwin" ]]
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-then
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- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=ACT"
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- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
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- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
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-fi
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-
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if [[ "$QUIET" = no ]]
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then
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echo "Starting ACT with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
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fi
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-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ActMain $*
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+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/act.jar $*
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result=$?
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exit $result
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--- a/art
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+++ b/art
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@@ -44,36 +44,6 @@
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exit 0
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}
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-add_proxy_properties() {
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_PROXY
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- fi
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_proxy
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- fi
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-
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- if [[ "$http_proxy" != "" ]]
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- then
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- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
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- fi
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-}
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-
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-#
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-# Resolve script path (inc symlinks)
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-#
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-SOURCE="${BASH_SOURCE[0]}"
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-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
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- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
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- SOURCE="$(readlink "$SOURCE")"
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- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
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-done
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-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
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-
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-
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# Special Sanger override on chado PGUSER
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if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
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then
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@@ -99,28 +69,6 @@
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shift
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done
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-
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-JAR_NAME=artemis.jar
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-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
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-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
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-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
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-
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-#
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-# Use a custom Java version if necessary
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-#
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-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
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-then
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- JAVA=`which java`
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-else
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- JAVA_HOME=$ARTEMIS_JAVA_JRE
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- JAVA=$ARTEMIS_JAVA_JRE/bin/java
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-fi
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-
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-#
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-# Allow URLs to work from behind firewalls.
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-#
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-add_proxy_properties
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-
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#
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# "-mx2g" sets the maximum amount of memory to use.
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# This may need to be increased when dealing with large files
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@@ -139,20 +87,12 @@
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#
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FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
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-PLATTMP=`uname`
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-if [[ "$PLATTMP" = "Darwin" ]]
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-then
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- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Artemis"
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- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
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- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
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-fi
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-
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if [[ "$QUIET" = "no" ]]
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then
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echo "Starting Artemis with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
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fi
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-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.ArtemisMain $*
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+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/artemis.jar $*
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result=$?
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exit $result
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--- a/bamview
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+++ b/bamview
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@@ -6,57 +6,7 @@
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QUIET=no
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|
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-add_proxy_properties() {
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_PROXY
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- fi
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-
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- if [[ "$http_proxy" = "" ]]
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- then
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- http_proxy=$HTTP_proxy
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- fi
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-
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- if [[ "$http_proxy" != "" ]]
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- then
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- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
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- fi
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||||||
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-}
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-
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||||||
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-#
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||||||
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-# Resolve script path (inc symlinks)
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||||||
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-#
|
||||||
|
-SOURCE="${BASH_SOURCE[0]}"
|
||||||
|
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
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||||||
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- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||||
|
- SOURCE="$(readlink "$SOURCE")"
|
||||||
|
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||||
|
-done
|
||||||
|
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||||
|
-
|
||||||
|
-
|
||||||
|
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
|
||||||
|
-JAR_NAME=bamview.jar
|
||||||
|
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||||
|
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||||
|
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||||
|
-
|
||||||
|
-#
|
||||||
|
-# Use a custom Java version if necessary
|
||||||
|
-#
|
||||||
|
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||||
|
-then
|
||||||
|
- JAVA=`which java`
|
||||||
|
-else
|
||||||
|
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||||
|
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||||
|
-fi
|
||||||
|
-
|
||||||
|
-#
|
||||||
|
-# Allow URLs to work from behind firewalls.
|
||||||
|
-#
|
||||||
|
-add_proxy_properties
|
||||||
|
|
||||||
|
#
|
||||||
|
# "-mx2g" sets the maximum amount of memory to use.
|
||||||
|
@@ -69,20 +19,12 @@
|
||||||
|
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
|
||||||
|
fi
|
||||||
|
|
||||||
|
-PLATTMP=`uname`
|
||||||
|
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||||
|
-then
|
||||||
|
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
|
||||||
|
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||||
|
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||||
|
-fi
|
||||||
|
-
|
||||||
|
if [[ "$QUIET" = "no" ]]
|
||||||
|
then
|
||||||
|
echo "Starting BamView with arguments: $FLAGS $APPLICATION_PROPERTIES $*"
|
||||||
|
fi
|
||||||
|
|
||||||
|
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.components.alignment.BamView $*
|
||||||
|
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/bamview.jar $*
|
||||||
|
result=$?
|
||||||
|
|
||||||
|
exit $result
|
||||||
|
--- a/dnaplotter
|
||||||
|
+++ b/dnaplotter
|
||||||
|
@@ -25,37 +25,6 @@
|
||||||
|
exit 0
|
||||||
|
}
|
||||||
|
|
||||||
|
-add_proxy_properties() {
|
||||||
|
-
|
||||||
|
- if [[ "$http_proxy" = "" ]]
|
||||||
|
- then
|
||||||
|
- http_proxy=$HTTP_PROXY
|
||||||
|
- fi
|
||||||
|
-
|
||||||
|
- if [[ "$http_proxy" = "" ]]
|
||||||
|
- then
|
||||||
|
- http_proxy=$HTTP_proxy
|
||||||
|
- fi
|
||||||
|
-
|
||||||
|
- if [[ "$http_proxy" != "" ]]
|
||||||
|
- then
|
||||||
|
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -DproxySet=true "`echo $http_proxy | sed 's/http:\/\/\(.*\):\(.*\)/ -Dhttp.proxyHost=\1 -Dhttp.proxyPort=\2/'`
|
||||||
|
- fi
|
||||||
|
-}
|
||||||
|
-
|
||||||
|
-
|
||||||
|
-#
|
||||||
|
-# Resolve script path (inc symlinks)
|
||||||
|
-#
|
||||||
|
-SOURCE="${BASH_SOURCE[0]}"
|
||||||
|
-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
|
||||||
|
- DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
|
||||||
|
- SOURCE="$(readlink "$SOURCE")"
|
||||||
|
- [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
|
||||||
|
-done
|
||||||
|
-APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
|
||||||
|
-
|
||||||
|
-
|
||||||
|
#
|
||||||
|
# Parse arguments.
|
||||||
|
#
|
||||||
|
@@ -75,28 +44,6 @@
|
||||||
|
shift
|
||||||
|
done
|
||||||
|
|
||||||
|
-
|
||||||
|
-JAR_NAME=dnaplotter.jar
|
||||||
|
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
|
||||||
|
-JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
|
||||||
|
-ARTEMIS_CP=$APPLICATION_HOME:$JAR_FILE_DEFAULT:$JAR_FILE_INSTALLED
|
||||||
|
-
|
||||||
|
-#
|
||||||
|
-# Use a custom Java version if necessary
|
||||||
|
-#
|
||||||
|
-if [[ "$ARTEMIS_JAVA_JRE" = "" ]]
|
||||||
|
-then
|
||||||
|
- JAVA=`which java`
|
||||||
|
-else
|
||||||
|
- JAVA_HOME=$ARTEMIS_JAVA_JRE
|
||||||
|
- JAVA=$ARTEMIS_JAVA_JRE/bin/java
|
||||||
|
-fi
|
||||||
|
-
|
||||||
|
-#
|
||||||
|
-# Allow URLs to work from behind firewalls.
|
||||||
|
-#
|
||||||
|
-add_proxy_properties
|
||||||
|
-
|
||||||
|
#
|
||||||
|
# "-mx2g" sets the maximum amount of memory to use.
|
||||||
|
# This may need to be increased when dealing with large files
|
||||||
|
@@ -108,20 +55,12 @@
|
||||||
|
FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
|
||||||
|
fi
|
||||||
|
|
||||||
|
-PLATTMP=`uname`
|
||||||
|
-if [[ "$PLATTMP" = "Darwin" ]]
|
||||||
|
-then
|
||||||
|
- APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=Circular-Plot"
|
||||||
|
- JAR_FILE_MACAPP=$APPLICATION_HOME/Java/$JAR_NAME
|
||||||
|
- ARTEMIS_CP="$JAR_FILE_MACAPP:$ARTEMIS_CP"
|
||||||
|
-fi
|
||||||
|
-
|
||||||
|
if [[ "$QUIET" = "no" ]]
|
||||||
|
then
|
||||||
|
echo "Starting DNA Plotter with arguments: $FLAGS $APPLICATION_PROPERTIES $TEMPLATE_FILE_ARG"
|
||||||
|
fi
|
||||||
|
|
||||||
|
-$JAVA $FLAGS $APPLICATION_PROPERTIES -cp "$ARTEMIS_CP" uk.ac.sanger.artemis.circular.DNADraw $TEMPLATE_FILE_ARG
|
||||||
|
+java $FLAGS $APPLICATION_PROPERTIES -jar /usr/share/artemis/dnaplotter.jar $TEMPLATE_FILE_ARG
|
||||||
|
result=$?
|
||||||
|
|
||||||
|
exit $result
|
||||||
|
|
||||||
|
|
||||||
16
prepare/artemis/lilac.yaml
Normal file
16
prepare/artemis/lilac.yaml
Normal file
|
|
@ -0,0 +1,16 @@
|
||||||
|
build_prefix: extra-x86_64
|
||||||
|
maintainers:
|
||||||
|
- github: starsareintherose
|
||||||
|
email: kuoi@bioarchlinux.org
|
||||||
|
pre_build_script: |
|
||||||
|
update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
|
||||||
|
run_cmd(['updpkgsums'])
|
||||||
|
post_build_script: |
|
||||||
|
git_add_files('PKGBUILD')
|
||||||
|
git_commit()
|
||||||
|
update_aur_repo()
|
||||||
|
update_on:
|
||||||
|
- source: github
|
||||||
|
github: sanger-pathogens/Artemis
|
||||||
|
use_max_tag: true
|
||||||
|
prefix: 'v'
|
||||||
5
prepare/artemis/readme
Normal file
5
prepare/artemis/readme
Normal file
|
|
@ -0,0 +1,5 @@
|
||||||
|
# Artemis
|
||||||
|
|
||||||
|
art and act shell script doesn't work.
|
||||||
|
|
||||||
|
Fix it and then this package can work
|
||||||
Loading…
Add table
Reference in a new issue